1s autopkgtest [07:48:46]: starting date and time: 2024-03-21 07:48:46+0000 1s autopkgtest [07:48:46]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 1s autopkgtest [07:48:46]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.l6eqp95w/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:openjdk-lts,src:alsa-lib,src:cups,src:gnutls28,src:libpng1.6,src:nettle,src:wp2latex --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-lts/11.0.23~7ea-1ubuntu1 alsa-lib/1.2.11-1build1 cups/2.4.7-1.2ubuntu1 gnutls28/3.8.3-1.1ubuntu2 libpng1.6/1.6.43-3 nettle/3.9.1-2.2 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-18.secgroup --name adt-noble-ppc64el-bbmap-20240321-074846-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-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/ 188s autopkgtest [07:51:54]: testbed dpkg architecture: ppc64el 188s autopkgtest [07:51:54]: testbed apt version: 2.7.12 188s autopkgtest [07:51:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 189s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 190s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [492 kB] 190s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 190s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3769 kB] 190s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 190s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [671 kB] 190s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 190s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 190s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 190s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4114 kB] 191s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 191s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [58.3 kB] 191s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 194s Fetched 9295 kB in 3s (3705 kB/s) 194s Reading package lists... 197s Reading package lists... 197s Building dependency tree... 197s Reading state information... 197s Calculating upgrade... 198s The following packages will be upgraded: 198s debianutils linux-firmware 198s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 198s Need to get 476 MB of archives. 198s After this operation, 5724 kB of additional disk space will be used. 198s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el debianutils ppc64el 5.17 [90.4 kB] 198s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el linux-firmware ppc64el 20240318.git3b128b60-0ubuntu1 [475 MB] 217s Fetched 476 MB in 19s (25.5 MB/s) 217s (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 ... 70095 files and directories currently installed.) 217s Preparing to unpack .../debianutils_5.17_ppc64el.deb ... 217s Unpacking debianutils (5.17) over (5.16) ... 217s Setting up debianutils (5.17) ... 217s (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 ... 70095 files and directories currently installed.) 217s Preparing to unpack .../linux-firmware_20240318.git3b128b60-0ubuntu1_ppc64el.deb ... 217s Unpacking linux-firmware (20240318.git3b128b60-0ubuntu1) over (20240202.git36777504-0ubuntu1) ... 220s Setting up linux-firmware (20240318.git3b128b60-0ubuntu1) ... 220s Processing triggers for man-db (2.12.0-3) ... 222s Processing triggers for initramfs-tools (0.142ubuntu20) ... 222s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 222s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 229s Reading package lists... 229s Building dependency tree... 229s Reading state information... 229s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 230s sh: Attempting to set up Debian/Ubuntu apt sources automatically 230s sh: Distribution appears to be Ubuntu 231s Reading package lists... 231s Building dependency tree... 231s Reading state information... 231s eatmydata is already the newest version (131-1). 231s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 231s Reading package lists... 231s Building dependency tree... 231s Reading state information... 231s 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... 231s Building dependency tree... 231s Reading state information... 232s rng-tools-debian is already the newest version (2.4). 232s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 232s Reading package lists... 232s Building dependency tree... 232s Reading state information... 232s The following packages will be REMOVED: 232s cloud-init* python3-configobj* python3-debconf* 232s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 232s After this operation, 3252 kB disk space will be freed. 232s (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 ... 70157 files and directories currently installed.) 232s Removing cloud-init (24.1.1-0ubuntu1) ... 233s Removing python3-configobj (5.0.8-3) ... 233s Removing python3-debconf (1.5.86) ... 233s Processing triggers for man-db (2.12.0-3) ... 233s (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 ... 69768 files and directories currently installed.) 233s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 234s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 234s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 234s invoke-rc.d: policy-rc.d denied execution of try-restart. 234s Reading package lists... 234s Building dependency tree... 234s Reading state information... 234s linux-generic is already the newest version (6.8.0-11.11+1). 234s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 235s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 235s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 235s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 237s Reading package lists... 237s Reading package lists... 238s Building dependency tree... 238s Reading state information... 238s Calculating upgrade... 238s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 238s Reading package lists... 238s Building dependency tree... 238s Reading state information... 238s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 238s autopkgtest [07:52:44]: rebooting testbed after setup commands that affected boot 404s autopkgtest [07:55:30]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 407s autopkgtest [07:55:33]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 409s Get:1 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (dsc) [2286 B] 409s Get:2 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (tar) [5343 kB] 409s Get:3 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (diff) [25.4 kB] 409s gpgv: Signature made Fri Nov 24 11:00:29 2023 UTC 409s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 409s gpgv: issuer "emollier@debian.org" 409s gpgv: Can't check signature: No public key 409s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.06+dfsg-1.dsc: no acceptable signature found 410s autopkgtest [07:55:36]: testing package bbmap version 39.06+dfsg-1 410s autopkgtest [07:55:36]: build not needed 443s autopkgtest [07:56:09]: test run-unit-test: preparing testbed 445s Reading package lists... 446s Building dependency tree... 446s Reading state information... 446s Starting pkgProblemResolver with broken count: 0 446s Starting 2 pkgProblemResolver with broken count: 0 446s Done 446s The following additional packages will be installed: 446s bbmap bbmap-jni ca-certificates-java fontconfig-config fonts-dejavu-core 446s fonts-dejavu-mono java-common libapache-pom-java libasound2 libasound2-data 446s libavahi-client3 libavahi-common-data libavahi-common3 libcommons-cli-java 446s libcommons-codec-java libcommons-io-java libcommons-parent-java libcups2 446s libfontconfig1 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 446s liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 446s python-biopython-doc 446s Suggested packages: 446s default-jre libasound2-plugins alsa-utils libcommons-io-java-doc cups-common 446s liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd libnss-mdns 446s fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 446s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 446s Recommended packages: 446s pigz alsa-ucm-conf alsa-topology-conf python3-biopython 446s The following NEW packages will be installed: 446s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java fontconfig-config 446s fonts-dejavu-core fonts-dejavu-mono java-common libapache-pom-java 446s libasound2 libasound2-data libavahi-client3 libavahi-common-data 446s libavahi-common3 libcommons-cli-java libcommons-codec-java 446s libcommons-io-java libcommons-parent-java libcups2 libfontconfig1 446s libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 liblcms2-2 446s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 446s python-biopython-doc 446s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 446s Need to get 79.6 MB/79.6 MB of archives. 446s After this operation, 240 MB of additional disk space will be used. 446s Get:1 /tmp/autopkgtest.mRE6qJ/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [728 B] 446s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-cli-java all 1.6.0-1 [59.9 kB] 446s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libapache-pom-java all 29-2 [5284 B] 446s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-parent-java all 56-1 [10.7 kB] 446s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-codec-java all 1.16.0-1 [306 kB] 446s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-io-java all 2.11.0-2 [297 kB] 447s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblog4j1.2-java all 1.2.17-11 [439 kB] 447s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmpj-java all 0.44+dfsg-4 [443 kB] 447s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el ca-certificates-java all 20240118 [11.6 kB] 447s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el java-common all 0.75+exp1 [6798 B] 447s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-common-data ppc64el 0.8-13ubuntu2 [29.5 kB] 447s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-common3 ppc64el 0.8-13ubuntu2 [25.8 kB] 447s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-client3 ppc64el 0.8-13ubuntu2 [30.6 kB] 447s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libcups2 ppc64el 2.4.6-0ubuntu3 [344 kB] 447s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el liblcms2-2 ppc64el 2.14-2 [243 kB] 447s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 447s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 447s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 447s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 447s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 447s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 447s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libasound2-data all 1.2.10-3build1 [20.7 kB] 447s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libasound2 ppc64el 1.2.10-3build1 [496 kB] 447s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 447s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 447s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcsclite1 ppc64el 2.0.0-1 [27.9 kB] 447s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el openjdk-17-jre-headless ppc64el 17.0.10+7-1 [47.2 MB] 448s Get:28 http://ftpmaster.internal/ubuntu noble/universe ppc64el bbmap all 39.06+dfsg-1 [9768 kB] 448s Get:29 http://ftpmaster.internal/ubuntu noble/universe ppc64el bbmap-jni ppc64el 39.06+dfsg-1 [32.8 kB] 448s Get:30 http://ftpmaster.internal/ubuntu noble/universe ppc64el python-biopython-doc all 1.81+dfsg-3 [17.3 MB] 449s Fetched 79.6 MB in 3s (29.5 MB/s) 449s Selecting previously unselected package libcommons-cli-java. 449s (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 ... 69713 files and directories currently installed.) 449s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 449s Unpacking libcommons-cli-java (1.6.0-1) ... 449s Selecting previously unselected package libapache-pom-java. 449s Preparing to unpack .../01-libapache-pom-java_29-2_all.deb ... 449s Unpacking libapache-pom-java (29-2) ... 449s Selecting previously unselected package libcommons-parent-java. 449s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 449s Unpacking libcommons-parent-java (56-1) ... 449s Selecting previously unselected package libcommons-codec-java. 449s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 449s Unpacking libcommons-codec-java (1.16.0-1) ... 449s Selecting previously unselected package libcommons-io-java. 449s Preparing to unpack .../04-libcommons-io-java_2.11.0-2_all.deb ... 449s Unpacking libcommons-io-java (2.11.0-2) ... 449s Selecting previously unselected package liblog4j1.2-java. 449s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 449s Unpacking liblog4j1.2-java (1.2.17-11) ... 449s Selecting previously unselected package libmpj-java. 449s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 449s Unpacking libmpj-java (0.44+dfsg-4) ... 449s Selecting previously unselected package ca-certificates-java. 449s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 449s Unpacking ca-certificates-java (20240118) ... 449s Selecting previously unselected package java-common. 449s Preparing to unpack .../08-java-common_0.75+exp1_all.deb ... 449s Unpacking java-common (0.75+exp1) ... 449s Selecting previously unselected package libavahi-common-data:ppc64el. 449s Preparing to unpack .../09-libavahi-common-data_0.8-13ubuntu2_ppc64el.deb ... 449s Unpacking libavahi-common-data:ppc64el (0.8-13ubuntu2) ... 449s Selecting previously unselected package libavahi-common3:ppc64el. 449s Preparing to unpack .../10-libavahi-common3_0.8-13ubuntu2_ppc64el.deb ... 449s Unpacking libavahi-common3:ppc64el (0.8-13ubuntu2) ... 449s Selecting previously unselected package libavahi-client3:ppc64el. 449s Preparing to unpack .../11-libavahi-client3_0.8-13ubuntu2_ppc64el.deb ... 449s Unpacking libavahi-client3:ppc64el (0.8-13ubuntu2) ... 449s Selecting previously unselected package libcups2:ppc64el. 449s Preparing to unpack .../12-libcups2_2.4.6-0ubuntu3_ppc64el.deb ... 449s Unpacking libcups2:ppc64el (2.4.6-0ubuntu3) ... 449s Selecting previously unselected package liblcms2-2:ppc64el. 449s Preparing to unpack .../13-liblcms2-2_2.14-2_ppc64el.deb ... 449s Unpacking liblcms2-2:ppc64el (2.14-2) ... 450s Selecting previously unselected package libjpeg-turbo8:ppc64el. 450s Preparing to unpack .../14-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 450s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 450s Selecting previously unselected package libjpeg8:ppc64el. 450s Preparing to unpack .../15-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 450s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 450s Selecting previously unselected package fonts-dejavu-mono. 450s Preparing to unpack .../16-fonts-dejavu-mono_2.37-8_all.deb ... 450s Unpacking fonts-dejavu-mono (2.37-8) ... 450s Selecting previously unselected package fonts-dejavu-core. 450s Preparing to unpack .../17-fonts-dejavu-core_2.37-8_all.deb ... 450s Unpacking fonts-dejavu-core (2.37-8) ... 450s Selecting previously unselected package fontconfig-config. 450s Preparing to unpack .../18-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 450s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 450s Selecting previously unselected package libfontconfig1:ppc64el. 450s Preparing to unpack .../19-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 450s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 450s Selecting previously unselected package libasound2-data. 450s Preparing to unpack .../20-libasound2-data_1.2.10-3build1_all.deb ... 450s Unpacking libasound2-data (1.2.10-3build1) ... 450s Selecting previously unselected package libasound2:ppc64el. 450s Preparing to unpack .../21-libasound2_1.2.10-3build1_ppc64el.deb ... 450s Unpacking libasound2:ppc64el (1.2.10-3build1) ... 450s Selecting previously unselected package libgraphite2-3:ppc64el. 450s Preparing to unpack .../22-libgraphite2-3_1.3.14-2_ppc64el.deb ... 450s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 450s Selecting previously unselected package libharfbuzz0b:ppc64el. 450s Preparing to unpack .../23-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 450s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 450s Selecting previously unselected package libpcsclite1:ppc64el. 450s Preparing to unpack .../24-libpcsclite1_2.0.0-1_ppc64el.deb ... 450s Unpacking libpcsclite1:ppc64el (2.0.0-1) ... 450s Selecting previously unselected package openjdk-17-jre-headless:ppc64el. 450s Preparing to unpack .../25-openjdk-17-jre-headless_17.0.10+7-1_ppc64el.deb ... 450s Unpacking openjdk-17-jre-headless:ppc64el (17.0.10+7-1) ... 451s Selecting previously unselected package bbmap. 451s Preparing to unpack .../26-bbmap_39.06+dfsg-1_all.deb ... 451s Unpacking bbmap (39.06+dfsg-1) ... 451s Selecting previously unselected package bbmap-jni. 451s Preparing to unpack .../27-bbmap-jni_39.06+dfsg-1_ppc64el.deb ... 451s Unpacking bbmap-jni (39.06+dfsg-1) ... 451s Selecting previously unselected package python-biopython-doc. 451s Preparing to unpack .../28-python-biopython-doc_1.81+dfsg-3_all.deb ... 451s Unpacking python-biopython-doc (1.81+dfsg-3) ... 451s Selecting previously unselected package autopkgtest-satdep. 451s Preparing to unpack .../29-1-autopkgtest-satdep.deb ... 451s Unpacking autopkgtest-satdep (0) ... 451s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 451s Setting up liblcms2-2:ppc64el (2.14-2) ... 451s Setting up java-common (0.75+exp1) ... 451s Setting up libcommons-cli-java (1.6.0-1) ... 451s Setting up liblog4j1.2-java (1.2.17-11) ... 451s Setting up libasound2-data (1.2.10-3build1) ... 451s Setting up libapache-pom-java (29-2) ... 451s Setting up libavahi-common-data:ppc64el (0.8-13ubuntu2) ... 451s Setting up fonts-dejavu-mono (2.37-8) ... 451s Setting up fonts-dejavu-core (2.37-8) ... 451s Setting up libpcsclite1:ppc64el (2.0.0-1) ... 451s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 451s Setting up python-biopython-doc (1.81+dfsg-3) ... 451s Setting up libasound2:ppc64el (1.2.10-3build1) ... 451s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 451s Setting up bbmap-jni (39.06+dfsg-1) ... 451s Setting up ca-certificates-java (20240118) ... 451s No JRE found. Skipping Java certificates setup. 451s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 451s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 452s Setting up libcommons-parent-java (56-1) ... 452s Setting up libavahi-common3:ppc64el (0.8-13ubuntu2) ... 452s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 452s Setting up libcommons-codec-java (1.16.0-1) ... 452s Setting up libavahi-client3:ppc64el (0.8-13ubuntu2) ... 452s Setting up libcommons-io-java (2.11.0-2) ... 452s Setting up libmpj-java (0.44+dfsg-4) ... 452s Setting up libcups2:ppc64el (2.4.6-0ubuntu3) ... 452s Setting up openjdk-17-jre-headless:ppc64el (17.0.10+7-1) ... 452s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/java to provide /usr/bin/java (java) in auto mode 452s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 452s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 452s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 452s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 452s Processing triggers for libc-bin (2.39-0ubuntu2) ... 452s Processing triggers for man-db (2.12.0-3) ... 453s Processing triggers for ca-certificates-java (20240118) ... 453s Adding debian:ACCVRAIZ1.pem 453s Adding debian:AC_RAIZ_FNMT-RCM.pem 453s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 453s Adding debian:ANF_Secure_Server_Root_CA.pem 453s Adding debian:Actalis_Authentication_Root_CA.pem 453s Adding debian:AffirmTrust_Commercial.pem 453s Adding debian:AffirmTrust_Networking.pem 453s Adding debian:AffirmTrust_Premium.pem 453s Adding debian:AffirmTrust_Premium_ECC.pem 453s Adding debian:Amazon_Root_CA_1.pem 453s Adding debian:Amazon_Root_CA_2.pem 453s Adding debian:Amazon_Root_CA_3.pem 453s Adding debian:Amazon_Root_CA_4.pem 453s Adding debian:Atos_TrustedRoot_2011.pem 453s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 453s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 453s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 453s Adding debian:BJCA_Global_Root_CA1.pem 453s Adding debian:BJCA_Global_Root_CA2.pem 453s Adding debian:Baltimore_CyberTrust_Root.pem 453s Adding debian:Buypass_Class_2_Root_CA.pem 453s Adding debian:Buypass_Class_3_Root_CA.pem 453s Adding debian:CA_Disig_Root_R2.pem 453s Adding debian:CFCA_EV_ROOT.pem 453s Adding debian:COMODO_Certification_Authority.pem 453s Adding debian:COMODO_ECC_Certification_Authority.pem 453s Adding debian:COMODO_RSA_Certification_Authority.pem 453s Adding debian:Certainly_Root_E1.pem 453s Adding debian:Certainly_Root_R1.pem 453s Adding debian:Certigna.pem 453s Adding debian:Certigna_Root_CA.pem 453s Adding debian:Certum_EC-384_CA.pem 453s Adding debian:Certum_Trusted_Network_CA.pem 453s Adding debian:Certum_Trusted_Network_CA_2.pem 453s Adding debian:Certum_Trusted_Root_CA.pem 453s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 453s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 453s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 453s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 453s Adding debian:Comodo_AAA_Services_root.pem 453s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 453s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 453s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 453s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 453s Adding debian:DigiCert_Assured_ID_Root_CA.pem 453s Adding debian:DigiCert_Assured_ID_Root_G2.pem 453s Adding debian:DigiCert_Assured_ID_Root_G3.pem 453s Adding debian:DigiCert_Global_Root_CA.pem 453s Adding debian:DigiCert_Global_Root_G2.pem 453s Adding debian:DigiCert_Global_Root_G3.pem 453s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 453s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 453s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 453s Adding debian:DigiCert_Trusted_Root_G4.pem 453s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 453s Adding debian:Entrust_Root_Certification_Authority.pem 453s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 453s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 453s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 453s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 453s Adding debian:GLOBALTRUST_2020.pem 454s Adding debian:GTS_Root_R1.pem 454s Adding debian:GTS_Root_R2.pem 454s Adding debian:GTS_Root_R3.pem 454s Adding debian:GTS_Root_R4.pem 454s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 454s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 454s Adding debian:GlobalSign_Root_CA.pem 454s Adding debian:GlobalSign_Root_CA_-_R3.pem 454s Adding debian:GlobalSign_Root_CA_-_R6.pem 454s Adding debian:GlobalSign_Root_E46.pem 454s Adding debian:GlobalSign_Root_R46.pem 454s Adding debian:Go_Daddy_Class_2_CA.pem 454s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 454s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 454s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 454s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 454s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 454s Adding debian:HiPKI_Root_CA_-_G1.pem 454s Adding debian:Hongkong_Post_Root_CA_3.pem 454s Adding debian:ISRG_Root_X1.pem 454s Adding debian:ISRG_Root_X2.pem 454s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 454s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 454s Adding debian:Izenpe.com.pem 454s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 454s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 454s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 454s Adding debian:NAVER_Global_Root_Certification_Authority.pem 454s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 454s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 454s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 454s Adding debian:QuoVadis_Root_CA_1_G3.pem 454s Adding debian:QuoVadis_Root_CA_2.pem 454s Adding debian:QuoVadis_Root_CA_2_G3.pem 454s Adding debian:QuoVadis_Root_CA_3.pem 454s Adding debian:QuoVadis_Root_CA_3_G3.pem 454s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 454s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 454s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 454s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 454s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 454s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 454s Adding debian:SZAFIR_ROOT_CA2.pem 454s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 454s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 454s Adding debian:SecureSign_RootCA11.pem 454s Adding debian:SecureTrust_CA.pem 454s Adding debian:Secure_Global_CA.pem 454s Adding debian:Security_Communication_ECC_RootCA1.pem 454s Adding debian:Security_Communication_RootCA2.pem 454s Adding debian:Security_Communication_RootCA3.pem 454s Adding debian:Security_Communication_Root_CA.pem 454s Adding debian:Starfield_Class_2_CA.pem 454s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 454s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 454s Adding debian:SwissSign_Gold_CA_-_G2.pem 454s Adding debian:SwissSign_Silver_CA_-_G2.pem 454s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 454s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 454s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 454s Adding debian:TWCA_Global_Root_CA.pem 454s Adding debian:TWCA_Root_Certification_Authority.pem 454s Adding debian:TeliaSonera_Root_CA_v1.pem 454s Adding debian:Telia_Root_CA_v2.pem 454s Adding debian:TrustAsia_Global_Root_CA_G3.pem 454s Adding debian:TrustAsia_Global_Root_CA_G4.pem 454s Adding debian:Trustwave_Global_Certification_Authority.pem 454s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 454s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 454s Adding debian:TunTrust_Root_CA.pem 454s Adding debian:UCA_Extended_Validation_Root.pem 454s Adding debian:UCA_Global_G2_Root.pem 454s Adding debian:USERTrust_ECC_Certification_Authority.pem 454s Adding debian:USERTrust_RSA_Certification_Authority.pem 454s Adding debian:XRamp_Global_CA_Root.pem 454s Adding debian:certSIGN_ROOT_CA.pem 454s Adding debian:certSIGN_Root_CA_G2.pem 454s Adding debian:e-Szigno_Root_CA_2017.pem 454s Adding debian:ePKI_Root_Certification_Authority.pem 454s Adding debian:emSign_ECC_Root_CA_-_C3.pem 454s Adding debian:emSign_ECC_Root_CA_-_G3.pem 454s Adding debian:emSign_Root_CA_-_C1.pem 454s Adding debian:emSign_Root_CA_-_G1.pem 454s Adding debian:vTrus_ECC_Root_CA.pem 454s Adding debian:vTrus_Root_CA.pem 454s done. 454s Setting up bbmap (39.06+dfsg-1) ... 454s Setting up autopkgtest-satdep (0) ... 456s (Reading database ... 72552 files and directories currently installed.) 456s Removing autopkgtest-satdep (0) ... 457s autopkgtest [07:56:23]: test run-unit-test: [----------------------- 457s 457s # bbmap 457s bbmap.sh --version 457s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 457s java -ea -Xmx2636m -Xms2636m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 457s BBMap version 39.06 457s For help, please run the shellscript with no parameters, or look in /docs/. 457s bbmap.sh --help 457s 457s BBMap 457s Written by Brian Bushnell, from Dec. 2010 - present 457s Last modified September 15, 2022 457s 457s Description: Fast and accurate splice-aware read aligner. 457s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 457s 457s To index: bbmap.sh ref= 457s To map: bbmap.sh in= out= 457s To map without writing an index: 457s bbmap.sh ref= in= out= nodisk 457s 457s in=stdin will accept reads from standard in, and out=stdout will write to 457s standard out, but file extensions are still needed to specify the format of the 457s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 457s standard in; out=stdout.sam.gz will write gzipped sam. 457s 457s Indexing Parameters (required when building the index): 457s nodisk=f Set to true to build index in memory and write nothing 457s to disk except output. 457s ref= Specify the reference sequence. Only do this ONCE, 457s when building the index (unless using 'nodisk'). 457s build=1 If multiple references are indexed in the same directory, 457s each needs a unique numeric ID (unless using 'nodisk'). 457s k=13 Kmer length, range 8-15. Longer is faster but uses 457s more memory. Shorter is more sensitive. 457s If indexing and mapping are done in two steps, K should 457s be specified each time. 457s path=<.> Specify the location to write the index, if you don't 457s want it in the current working directory. 457s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 457s number (reduces RAM by 50% and sensitivity slightly). 457s Should be enabled both when building the index AND 457s when mapping. 457s rebuild=f Force a rebuild of the index (ref= should be set). 457s 457s Input Parameters: 457s build=1 Designate index to use. Corresponds to the number 457s specified when building the index. 457s in= Primary reads input; required parameter. 457s in2= For paired reads in two files. 457s interleaved=auto True forces paired/interleaved input; false forces 457s single-ended mapping. If not specified, interleaved 457s status will be autodetected from read names. 457s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 457s BBMap and 6000 for BBMapPacBio. Only works for FASTA 457s input (use 'maxlen' for FASTQ input). The default for 457s bbmap.sh is 500, and for mapPacBio.sh is 6000. 457s unpigz=f Spawn a pigz (parallel gzip) process for faster 457s decompression than using Java. 457s Requires pigz to be installed. 457s touppercase=t (tuc) Convert lowercase letters in reads to upper case 457s (otherwise they will not match the reference). 457s 457s Sampling Parameters: 457s 457s reads=-1 Set to a positive number N to only process the first N 457s reads (or pairs), then quit. -1 means use all reads. 457s samplerate=1 Set to a number from 0 to 1 to randomly select that 457s fraction of reads for mapping. 1 uses all reads. 457s skipreads=0 Set to a number N to skip the first N reads (or pairs), 457s then map the rest. 457s 457s Mapping Parameters: 457s fast=f This flag is a macro which sets other paramters to run 457s faster, at reduced sensitivity. Bad for RNA-seq. 457s slow=f This flag is a macro which sets other paramters to run 457s slower, at greater sensitivity. 'vslow' is even slower. 457s maxindel=16000 Don't look for indels longer than this. Lower is faster. 457s Set to >=100k for RNAseq with long introns like mammals. 457s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 457s By default these are not sought, but may be found anyway. 457s tipsearch=100 Look this far for read-end deletions with anchors 457s shorter than K, using brute force. 457s minid=0.76 Approximate minimum alignment identity to look for. 457s Higher is faster and less sensitive. 457s minhits=1 Minimum number of seed hits required for candidate sites. 457s Higher is faster. 457s local=f Set to true to use local, rather than global, alignments. 457s This will soft-clip ugly ends of poor alignments. 457s perfectmode=f Allow only perfect mappings when set to true (very fast). 457s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 457s N's in the reference) mappings. 457s threads=auto (t) Set to number of threads desired. By default, uses 457s all cores available. 457s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 457s multiple top-scoring mapping locations). 457s best (use the first best site) 457s toss (consider unmapped) 457s random (select one top-scoring site randomly) 457s all (retain all top-scoring sites) 457s samestrandpairs=f (ssp) Specify whether paired reads should map to the 457s same strand or opposite strands. 457s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 457s orientation. Set to false for long-mate-pair libraries. 457s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 457s insert size or orientation, the read with the lower 457s mapping quality is marked unmapped. 457s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 457s be sent to 'outu' but not 'outm'. 457s rcomp=f Reverse complement both reads prior to mapping (for LMP 457s outward-facing libraries). 457s rcompmate=f Reverse complement read2 prior to mapping. 457s pairlen=32000 Set max allowed distance between paired reads. 457s (insert size)=(pairlen)+(read1 length)+(read2 length) 457s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 457s greater than this. Lower is faster. 457s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 457s is faster. 457s averagepairdist=100 (apd) Initial average distance between paired reads. 457s Varies dynamically; does not need to be specified. 457s deterministic=f Run in deterministic mode. In this case it is good 457s to set averagepairdist. BBMap is deterministic 457s without this flag if using single-ended reads, 457s or run singlethreaded. 457s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 457s fraction of read length. Faster but less accurate. 457s bandwidth=0 (bw) Set the bandwidth directly. 457s fraction of read length. Faster but less accurate. 457s usejni=f (jni) Do alignments faster, in C code. Requires 457s compiling the C code; details are in /jni/README.txt. 457s maxsites2=800 Don't analyze (or print) more than this many alignments 457s per read. 457s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 457s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 457s will ignore the most common 3% of kmers. 457s greedy=t Use a greedy algorithm to discard the least-useful 457s kmers on a per-read basis. 457s kfilter=0 If positive, potential mapping sites must have at 457s least this many consecutive exact matches. 457s 457s 457s Quality and Trimming Parameters: 457s bbmap.sh ref=example.fasta 457s qin=auto Set to 33 or 64 to specify input quality value ASCII 457s offset. 33 is Sanger, 64 is old Solexa. 457s qout=auto Set to 33 or 64 to specify output quality value ASCII 457s offset (only if output format is fastq). 457s qtrim=f Quality-trim ends before mapping. Options are: 457s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 457s untrim=f Undo trimming after mapping. Untrimmed bases will be 457s soft-clipped in cigar strings. 457s trimq=6 Trim regions with average quality below this 457s (phred algorithm). 457s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 457s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 457s quality strings for fasta input reads. 457s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 457s out-of-range quality values. 457s usequality=t Use quality scores when determining which read kmers 457s to use as seeds. 457s minaveragequality=0 (maq) Do not map reads with average quality below this. 457s maqb=0 If positive, calculate maq from this many initial bases. 457s 457s Output Parameters: 457s out= Write all reads to this file. 457s outu= Write only unmapped reads to this file. Does not 457s include unmapped paired reads with a mapped mate. 457s outm= Write only mapped reads to this file. Includes 457s unmapped paired reads with a mapped mate. 457s mappedonly=f If true, treats 'out' like 'outm'. 457s bamscript= (bs) Write a shell script to that will turn 457s the sam output into a sorted, indexed bam file. 457s ordered=f Set to true to output reads in same order as input. 457s Slower and uses more memory. 457s overwrite=f (ow) Allow process to overwrite existing files. 457s secondary=f Print secondary alignments. 457s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 457s with score of at least this fraction of primary. 457s ssao=f (secondarysiteasambiguousonly) Only print secondary 457s alignments for ambiguously-mapped reads. 457s maxsites=5 Maximum number of total alignments to print per read. 457s Only relevant when secondary=t. 457s quickmatch=f Generate cigar strings more quickly. 457s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 457s assuming that the remainder is a comment or description. 457s ziplevel=2 (zl) Compression level for zip or gzip output. 457s pigz=f Spawn a pigz (parallel gzip) process for faster 457s compression than Java. Requires pigz to be installed. 457s machineout=f Set to true to output statistics in machine-friendly 457s 'key=value' format. 457s printunmappedcount=f Print the total number of unmapped reads and bases. 457s If input is paired, the number will be of pairs 457s for which both reads are unmapped. 457s showprogress=0 If positive, print a '.' every X reads. 457s showprogress2=0 If positive, print the number of seconds since the 457s last progress update (instead of a '.'). 457s renamebyinsert=f Renames reads based on their mapped insert size. 457s 457s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 457s bloom=f Use a Bloom filter to ignore reads not sharing kmers 457s with the reference. This uses more memory, but speeds 457s mapping when most reads don't match the reference. 457s bloomhashes=2 Number of hash functions. 457s bloomminhits=3 Number of consecutive hits to be considered matched. 457s bloomk=31 Bloom filter kmer length. 457s bloomserial=t Use the serialized Bloom filter for greater loading 457s speed, if available. If not, generate and write one. 457s 457s Post-Filtering Parameters: 457s idfilter=0 Independant of minid; sets exact minimum identity 457s allowed for alignments to be printed. Range 0 to 1. 457s subfilter=-1 Ban alignments with more than this many substitutions. 457s insfilter=-1 Ban alignments with more than this many insertions. 457s delfilter=-1 Ban alignments with more than this many deletions. 457s indelfilter=-1 Ban alignments with more than this many indels. 457s editfilter=-1 Ban alignments with more than this many edits. 457s inslenfilter=-1 Ban alignments with an insertion longer than this. 457s dellenfilter=-1 Ban alignments with a deletion longer than this. 457s nfilter=-1 Ban alignments with more than this many ns. This 457s includes nocall, noref, and off scaffold ends. 457s 457s Sam flags and settings: 457s noheader=f Disable generation of header lines. 457s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 457s with = and X, or 1.3 to use M. 457s saa=t (secondaryalignmentasterisks) Use asterisks instead of 457s bases for sam secondary alignments. 457s cigar=t Set to 'f' to skip generation of cigar strings (faster). 457s keepnames=f Keep original names of paired reads, rather than 457s ensuring both reads have the same name. 457s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 457s cigar strings for deletions of at least that length. 457s rgid= Set readgroup ID. All other readgroup fields 457s can be set similarly, with the flag rgXX= 457s If you set a readgroup flag to the word 'filename', 457s e.g. rgid=filename, the input file name will be used. 457s mdtag=f Write MD tags. 457s nhtag=f Write NH tags. 457s xmtag=f Write XM tags (may only work correctly with ambig=all). 457s amtag=f Write AM tags. 457s nmtag=f Write NM tags. 457s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 457s for RNAseq using firststrand, secondstrand, or 457s unstranded libraries. Needed by Cufflinks. 457s JGI mainly uses 'firststrand'. 457s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 457s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 457s prefixed by YL:Z: 457s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 457s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 457s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 457s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 457s boundstag=f Write a tag indicating whether either read in the pair 457s goes off the end of the reference, prefixed by XB:Z: 457s notags=f Turn off all optional tags. 457s 457s Histogram and statistics output parameters: 457s scafstats= Statistics on how many reads mapped to which scaffold. 457s refstats= Statistics on how many reads mapped to which reference 457s file; only for BBSplit. 457s sortscafs=t Sort scaffolds or references by read count. 457s bhist= Base composition histogram by position. 457s qhist= Quality histogram by position. 457s aqhist= Histogram of average read quality. 457s bqhist= Quality histogram designed for box plots. 457s lhist= Read length histogram. 457s ihist= Write histogram of insert sizes (for paired reads). 457s ehist= Errors-per-read histogram. 457s qahist= Quality accuracy histogram of error rates versus 457s quality score. 457s indelhist= Indel length histogram. 457s mhist= Histogram of match, sub, del, and ins rates by 457s read location. 457s gchist= Read GC content histogram. 457s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 457s gcpairs=t Use average GC of paired reads. 457s idhist= Histogram of read count versus percent identity. 457s idbins=100 Number idhist bins. Set to 'auto' to use read length. 457s statsfile=stderr Mapping statistics are printed here. 457s 457s Coverage output parameters (these may reduce speed and use more RAM): 457s covstats= Per-scaffold coverage info. 457s rpkm= Per-scaffold RPKM/FPKM counts. 457s covhist= Histogram of # occurrences of each depth level. 457s basecov= Coverage per base location. 457s bincov= Print binned coverage per location (one line per X bases). 457s covbinsize=1000 Set the binsize for binned coverage output. 457s nzo=t Only print scaffolds with nonzero coverage. 457s twocolumn=f Change to true to print only ID and Avg_fold instead of 457s all 6 columns to the 'out=' file. 457s 32bit=f Set to true if you need per-base coverage over 64k. 457s strandedcov=f Track coverage for plus and minus strand independently. 457s startcov=f Only track start positions of reads. 457s secondarycov=t Include coverage of secondary alignments. 457s physcov=f Calculate physical coverage for paired reads. 457s This includes the unsequenced bases. 457s delcoverage=t (delcov) Count bases covered by deletions as covered. 457s True is faster than false. 457s covk=0 If positive, calculate kmer coverage statistics. 457s 457s Java Parameters: 457s -Xmx This will set Java's memory usage, 457s overriding autodetection. 457s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 457s will specify 800 megs. The max is typically 85% of 457s physical memory. The human genome requires around 24g, 457s or 12g with the 'usemodulo' flag. The index uses 457s roughly 6 bytes per reference base. 457s -eoom This flag will cause the process to exit if an 457s out-of-memory exception occurs. Requires Java 8u92+. 457s -da Disable assertions. 457s 457s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 457s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 457s 457s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 457s java -ea -Xmx2635m -Xms2635m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 457s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 457s Version 39.06 457s 457s No output file. 457s Writing reference. 457s Executing dna.FastaToChromArrays2 [example.fasta, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=true, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=false] 457s 457s Set genScaffoldInfo=true 458s Writing chunk 1 458s Set genome to 1 458s 458s Loaded Reference: 0.005 seconds. 458s Loading index for chunk 1-1, build 1 458s No index available; generating from reference genome: /tmp/autopkgtest.mRE6qJ/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 458s Indexing threads started for block 0-1 458s Indexing threads finished for block 0-1 459s Generated Index: 1.342 seconds. 459s No reads to process; quitting. 459s 459s Total time: 1.517 seconds. 459s test -d ref 459s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 459s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 459s java -ea -Xmx2635m -Xms2635m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 459s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 459s Version 39.06 459s 459s Retaining first best site only for ambiguous mappings. 459s Set genome to 1 459s 459s Loaded Reference: 0.026 seconds. 459s Loading index for chunk 1-1, build 1 460s Generated Index: 0.489 seconds. 463s Analyzed Index: 3.770 seconds. 463s Started output stream: 0.023 seconds. 464s Cleared Memory: 0.111 seconds. 464s Processing reads in single-ended mode. 464s Started read stream. 464s Started 4 mapping threads. 464s Detecting finished threads: 0, 1, 2, 3 464s 464s ------------------ Results ------------------ 464s 464s Genome: 1 464s Key Length: 13 464s Max Indel: 16000 464s Minimum Score Ratio: 0.56 464s Mapping Mode: normal 464s Reads Used: 4 (153 bases) 464s 464s Mapping: 0.083 seconds. 464s Reads/sec: 47.95 464s kBases/sec: 1.83 464s 464s 464s Read 1 data: pct reads num reads pct bases num bases 464s 464s mapped: 0.0000% 0 0.0000% 0 464s unambiguous: 0.0000% 0 0.0000% 0 464s ambiguous: 0.0000% 0 0.0000% 0 464s low-Q discards: 25.0000% 1 19.6078% 30 464s 464s perfect best site: 0.0000% 0 0.0000% 0 464s semiperfect site: 0.0000% 0 0.0000% 0 464s 464s Match Rate: NA NA NaN% 0 464s Error Rate: NaN% 0 NaN% 0 464s Sub Rate: NaN% 0 NaN% 0 464s Del Rate: NaN% 0 NaN% 0 464s Ins Rate: NaN% 0 NaN% 0 464s N Rate: NaN% 0 NaN% 0 464s 464s Total time: 4.625 seconds. 464s test -r out.sam 464s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 464s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 464s java -ea -Xmx2636m -Xms2636m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 464s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 464s Version 39.06 464s 464s Retaining first best site only for ambiguous mappings. 464s Executing dna.FastaToChromArrays2 [example.fasta, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=false, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=true] 464s 464s Set genScaffoldInfo=true 464s Set genome to 1 464s 464s Loaded Reference: 0.002 seconds. 464s Loading index for chunk 1-1, build 1 464s Indexing threads started for block 0-1 464s Indexing threads finished for block 0-1 464s Generated Index: 0.233 seconds. 468s Analyzed Index: 3.744 seconds. 468s Started output stream: 0.061 seconds. 468s Cleared Memory: 0.112 seconds. 468s Processing reads in single-ended mode. 468s Started read stream. 468s Started 4 mapping threads. 468s Detecting finished threads: 0, 1, 2, 3 468s 468s ------------------ Results ------------------ 468s 468s Genome: 1 468s Key Length: 13 468s Max Indel: 16000 468s Minimum Score Ratio: 0.56 468s Mapping Mode: normal 468s Reads Used: 3 (75 bases) 468s 468s Mapping: 0.084 seconds. 468s Reads/sec: 35.63 468s kBases/sec: 0.89 468s 468s 468s Read 1 data: pct reads num reads pct bases num bases 468s 468s mapped: 100.0000% 3 100.0000% 75 468s unambiguous: 100.0000% 3 100.0000% 75 468s ambiguous: 0.0000% 0 0.0000% 0 468s low-Q discards: 0.0000% 0 0.0000% 0 468s 468s perfect best site: 100.0000% 3 100.0000% 75 468s semiperfect site: 100.0000% 3 100.0000% 75 468s 468s Match Rate: NA NA 100.0000% 75 468s Error Rate: 0.0000% 0 0.0000% 0 468s Sub Rate: 0.0000% 0 0.0000% 0 468s Del Rate: 0.0000% 0 0.0000% 0 468s Ins Rate: 0.0000% 0 0.0000% 0 468s N Rate: 0.0000% 0 0.0000% 0 468s 468s Total time: 4.373 seconds. 468s test -r out2.sam 468s 468s # bbduk 468s bbduk.sh --version 468s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 468s java -ea -Xmx1317m -Xms1317m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 468s BBMap version 39.06 468s For help, please run the shellscript with no parameters, or look in /docs/. 468s bbduk.sh --help 468s 468s Written by Brian Bushnell 468s Last modified November 9, 2023 468s 468s Description: Compares reads to the kmers in a reference dataset, optionally 468s allowing an edit distance. Splits the reads into two outputs - those that 468s match the reference, and those that don't. Can also trim (remove) the matching 468s parts of the reads rather than binning the reads. 468s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 468s 468s Usage: bbduk.sh in= out= ref= 468s 468s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 468s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 468s fasta input, set in=stdin.fa.gz 468s 468s Input parameters: 468s in= Main input. in=stdin.fq will pipe from stdin. 468s in2= Input for 2nd read of pairs in a different file. 468s ref= Comma-delimited list of reference files. 468s In addition to filenames, you may also use the keywords: 468s adapters, artifacts, phix, lambda, pjet, mtst, kapa 468s literal= Comma-delimited list of literal reference sequences. 468s touppercase=f (tuc) Change all bases upper-case. 468s interleaved=auto (int) t/f overrides interleaved autodetection. 468s Must be set mainually when streaming fastq input. 468s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 468s reads=-1 If positive, quit after processing X reads or pairs. 468s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 468s possible unambiguous copies. Intended for short motifs 468s or adapter barcodes, as time/memory use is exponential. 468s samplerate=1 Set lower to only process a fraction of input reads. 468s samref= Optional reference fasta for processing sam files. 468s 468s Output parameters: 468s out= (outnonmatch) Write reads here that do not contain 468s kmers matching the database. 'out=stdout.fq' will pipe 468s to standard out. 468s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 468s different file. 468s outm= (outmatch) Write reads here that fail filters. In default 468s kfilter mode, this means any read with a matching kmer. 468s In any mode, it also includes reads that fail filters such 468s as minlength, mingc, maxgc, entropy, etc. In other words, 468s it includes all reads that do not go to 'out'. 468s outm2= (outmatch2) Use this to write 2nd read of pairs to a 468s different file. 468s outs= (outsingle) Use this to write singleton reads whose mate 468s was trimmed shorter than minlen. 468s stats= Write statistics about which contamininants were detected. 468s refstats= Write statistics on a per-reference-file basis. 468s rpkm= Write RPKM for each reference sequence (for RNA-seq). 468s dump= Dump kmer tables to a file, in fasta format. 468s duk= Write statistics in duk's format. *DEPRECATED* 468s nzo=t Only write statistics about ref sequences with nonzero hits. 468s overwrite=t (ow) Grant permission to overwrite files. 468s showspeed=t (ss) 'f' suppresses display of processing speed. 468s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 468s fastawrap=70 Length of lines in fasta output. 468s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 468s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 468s 5 includes base counts. 468s rename=f Rename reads to indicate which sequences they matched. 468s refnames=f Use names of reference files rather than scaffold IDs. 468s trd=f Truncate read and ref names at the first whitespace. 468s ordered=f Set to true to output reads in same order as input. 468s maxbasesout=-1 If positive, quit after writing approximately this many 468s bases to out (outu/outnonmatch). 468s maxbasesoutm=-1 If positive, quit after writing approximately this many 468s bases to outm (outmatch). 468s json=f Print to screen in json format. 468s 468s Histogram output parameters: 468s bhist= Base composition histogram by position. 468s qhist= Quality histogram by position. 468s qchist= Count of bases with each quality value. 468s aqhist= Histogram of average read quality. 468s bqhist= Quality histogram designed for box plots. 468s lhist= Read length histogram. 468s phist= Polymer length histogram. 468s gchist= Read GC content histogram. 468s enthist= Read entropy histogram. 468s ihist= Insert size histogram, for paired reads in mapped sam. 468s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 468s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 468s more memory. The default is 6000 for some histograms 468s and 80000 for others. 468s 468s Histograms for mapped sam/bam files only: 468s histbefore=t Calculate histograms from reads before processing. 468s ehist= Errors-per-read histogram. 468s qahist= Quality accuracy histogram of error rates versus quality 468s score. 468s indelhist= Indel length histogram. 468s mhist= Histogram of match, sub, del, and ins rates by position. 468s idhist= Histogram of read count versus percent identity. 468s idbins=100 Number idhist bins. Set to 'auto' to use read length. 468s varfile= Ignore substitution errors listed in this file when 468s calculating error rates. Can be generated with 468s CallVariants. 468s vcf= Ignore substitution errors listed in this VCF file 468s when calculating error rates. 468s ignorevcfindels=t Also ignore indels listed in the VCF. 468s 468s Processing parameters: 468s k=27 Kmer length used for finding contaminants. Contaminants 468s shorter than k will not be found. k must be at least 1. 468s rcomp=t Look for reverse-complements of kmers in addition to 468s forward kmers. 468s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 468s increase sensitivity in the presence of errors. This may 468s also be set to a number, e.g. mm=3, to mask that many bp. 468s The default mm=t corresponds to mm=1 for odd-length kmers 468s and mm=2 for even-length kmers (as of v39.04), while 468s mm=f is always equivalent to mm=0. 468s minkmerhits=1 (mkh) Reads need at least this many matching kmers 468s to be considered as matching the reference. 468s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 468s kmers to hit a ref, in order to be considered a match. 468s If this and minkmerhits are set, the greater is used. 468s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 468s bases to be covered by ref kmers to be considered a match. 468s If specified, mcf overrides mkh and mkf. 468s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 468s Memory use is proportional to (3*K)^hdist. 468s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 468s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 468s and indels). Memory use is proportional to (8*K)^edist. 468s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 468s qhdist2=0 Sets qhdist for short kmers, when using mink. 468s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 468s forbidn=f (fn) Forbids matching of read kmers containing N. 468s By default, these will match a reference 'A' if 468s hdist>0 or edist>0, to increase sensitivity. 468s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 468s match (or either is trimmed shorter than minlen). 468s Set to false to require both. 468s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 468s This makes the statistics a bit odd. 468s findbestmatch=f (fbm) If multiple matches, associate read with sequence 468s sharing most kmers. Reduces speed. 468s skipr1=f Don't do kmer-based operations on read 1. 468s skipr2=f Don't do kmer-based operations on read 2. 468s ecco=f For overlapping paired reads only. Performs error- 468s correction with BBMerge prior to kmer operations. 468s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 468s matrices generated by CalcTrueQuality. 468s sam= If recalibration is desired, and matrices have not already 468s been generated, BBDuk will create them from the sam file. 468s amino=f Run in amino acid mode. Some features have not been 468s tested, but kmer-matching works fine. Maximum k is 12. 468s 468s Speed and Memory parameters: 468s threads=auto (t) Set number of threads to use; default is number of 468s logical processors. 468s prealloc=f Preallocate memory in table. Allows faster table loading 468s and more efficient memory usage, for a large reference. 468s monitor=f Kill this process if it crashes. monitor=600,0.01 would 468s kill after 600 seconds under 1% usage. 468s minrskip=1 (mns) Force minimal skip interval when indexing reference 468s kmers. 1 means use all, 2 means use every other kmer, etc. 468s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 468s reference kmers. Normally all are used for scaffolds<100kb, 468s but with longer scaffolds, up to maxrskip-1 are skipped. 468s rskip= Set both minrskip and maxrskip to the same value. 468s If not set, rskip will vary based on sequence length. 468s qskip=1 Skip query kmers to increase speed. 1 means use all. 468s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 468s reads and reference. Increases speed and reduces memory. 468s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 468s 468s Trimming/Filtering/Masking parameters: 468s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 468s All kmer processing modes are mutually exclusive. 468s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 468s 468s ktrim=f Trim reads to remove bases matching reference kmers, plus 468s all bases to the left or right. 468s Values: 468s f (don't trim), 468s r (trim to the right), 468s l (trim to the left) 468s ktrimtips=0 Set this to a positive number to perform ktrim on both 468s ends, examining only the outermost X bases. 468s kmask= Replace bases matching ref kmers with another symbol. 468s Allows any non-whitespace character, and processes short 468s kmers on both ends if mink is set. 'kmask=lc' will 468s convert masked bases to lowercase. 468s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 468s ksplit=f For single-ended reads only. Reads will be split into 468s pairs around the kmer. If the kmer is at the end of the 468s read, it will be trimmed instead. Singletons will go to 468s out, and pairs will go to outm. Do not use ksplit with 468s other operations such as quality-trimming or filtering. 468s mink=0 Look for shorter kmers at read tips down to this length, 468s when k-trimming or masking. 0 means disabled. Enabling 468s this will disable maskmiddle. 468s qtrim=f Trim read ends to remove bases with quality below trimq. 468s Performed AFTER looking for kmers. Values: 468s rl (trim both ends), 468s f (neither end), 468s r (right end only), 468s l (left end only), 468s w (sliding window). 468s trimq=6 Regions with average quality BELOW this will be trimmed, 468s if qtrim is set to something other than f. Can be a 468s floating-point number like 7.3. 468s trimclip=f Trim soft-clipped bases from sam files. 468s minlength=10 (ml) Reads shorter than this after trimming will be 468s discarded. Pairs will be discarded if both are shorter. 468s mlf=0 (minlengthfraction) Reads shorter than this fraction of 468s original length after trimming will be discarded. 468s maxlength= Reads longer than this after trimming will be discarded. 468s minavgquality=0 (maq) Reads with average quality (after trimming) below 468s this will be discarded. 468s maqb=0 If positive, calculate maq from this many initial bases. 468s minbasequality=0 (mbq) Reads with any base below this quality (after 468s trimming) will be discarded. 468s maxns=-1 If non-negative, reads with more Ns than this 468s (after trimming) will be discarded. 468s mcb=0 (minconsecutivebases) Discard reads without at least 468s this many consecutive called bases. 468s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 468s than minlength to outm rather than discarding. 468s tp=0 (trimpad) Trim this much extra around matching kmers. 468s tbo=f (trimbyoverlap) Trim adapters based on where paired 468s reads overlap. 468s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 468s minoverlap=14 Require this many bases of overlap for detection. 468s mininsert=40 Require insert size of at least this for overlap. 468s Should be reduced to 16 for small RNA sequencing. 468s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 468s reads to the minimum length of either. 468s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 468s (exclusive, 0-based). 468s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 468s (exclusive, 0-based). 468s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 468s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 468s modulo this number. 468s restrictleft=0 If positive, only look for kmer matches in the 468s leftmost X bases. 468s restrictright=0 If positive, only look for kmer matches in the 468s rightmost X bases. 468s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 468s both ends is desired, use ktrimtips. 468s mingc=0 Discard reads with GC content below this. 468s maxgc=1 Discard reads with GC content above this. 468s gcpairs=t Use average GC of paired reads. 468s Also affects gchist. 468s tossjunk=f Discard reads with invalid characters as bases. 468s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 468s 468s Header-parsing parameters - these require Illumina headers: 468s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 468s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 468s or barcodes containing 'N' otherwise. A barcode must be 468s the last part of the read header. Values: 468s t: Remove reads with bad barcodes. 468s f: Ignore barcodes. 468s crash: Crash upon encountering bad barcodes. 468s barcodes= Comma-delimited list of barcodes or files of barcodes. 468s xmin=-1 If positive, discard reads with a lesser X coordinate. 468s ymin=-1 If positive, discard reads with a lesser Y coordinate. 468s xmax=-1 If positive, discard reads with a greater X coordinate. 468s ymax=-1 If positive, discard reads with a greater Y coordinate. 468s 468s Polymer trimming: 468s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 468s at least this length on either end of reads. 468s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 468s length on the left end of reads. Does not trim poly-C. 468s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 468s length on the right end of reads. Does not trim poly-C. 468s trimpolyg=0 This sets both left and right at once. 468s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 468s at least this length (on the left). 468s Note: there are also equivalent poly-C flags. 468s 468s Polymer tracking: 468s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 468s plen=20 Length of homopolymers to count. 468s 468s Entropy/Complexity parameters: 468s entropy=-1 Set between 0 and 1 to filter reads with entropy below 468s that value. Higher is more stringent. 468s entropywindow=50 Calculate entropy using a sliding window of this length. 468s entropyk=5 Calculate entropy using kmers of this length. 468s minbasefrequency=0 Discard reads with a minimum base frequency below this. 468s entropytrim=f Values: 468s f: (false) Do not entropy-trim. 468s r: (right) Trim low entropy on the right end only. 468s l: (left) Trim low entropy on the left end only. 468s rl: (both) Trim low entropy on both ends. 468s entropymask=f Values: 468s f: (filter) Discard low-entropy sequences. 468s t: (true) Mask low-entropy parts of sequences with N. 468s lc: Change low-entropy parts of sequences to lowercase. 468s entropymark=f Mark each base with its entropy value. This is on a scale 468s of 0-41 and is reported as quality scores, so the output 468s should be fastq or fasta+qual. 468s NOTE: If set, entropytrim overrides entropymask. 468s 468s Cardinality estimation: 468s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 468s cardinalityout=f (loglogout) Count unique kmers in output reads. 468s loglogk=31 Use this kmer length for counting. 468s loglogbuckets=2048 Use this many buckets for counting. 468s khist= Kmer frequency histogram; plots number of kmers versus 468s kmer depth. This is approximate. 468s khistout= Kmer frequency histogram for output reads. 468s 468s Java Parameters: 468s 468s -Xmx This will set Java's memory usage, overriding autodetection. 468s -Xmx20g will 468s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 468s The max is typically 85% of physical memory. 468s -eoom This flag will cause the process to exit if an 468s out-of-memory exception occurs. Requires Java 8u92+. 468s -da Disable assertions. 468s 468s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 468s 468s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 468s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 468s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 468s java -ea -Xmx1317m -Xms1317m -cp /usr/share/java/bbmap.jar jgi.BBDuk in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 468s Executing jgi.BBDuk [in1=misc_dna_as_illumina.fastq, in2=misc_rna_as_illumina.fastq, qtrim=rl, trimq=15, minlen=75, out=out.fastq.gz] 468s Version 39.06 468s 469s 0.015 seconds. 469s Initial: 469s Memory: max=1409m, total=1409m, free=1379m, used=30m 469s 469s Input is being processed as paired 469s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 469s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 469s Started output streams: 0.017 seconds. 469s Processing time: 0.004 seconds. 469s 469s Input: 8 reads 306 bases. 469s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 469s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 469s Result: 0 reads (0.00%) 0 bases (0.00%) 469s 469s Time: 0.023 seconds. 469s Reads Processed: 8 0.34k reads/sec 469s Bases Processed: 306 0.01m bases/sec 469s test -r out.fastq.gz 469s 469s # bbnorm 469s bbnorm.sh --version 469s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 469s java -ea -Xmx2635m -Xms2635m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 469s BBMap version 39.06 469s For help, please run the shellscript with no parameters, or look in /docs/. 469s bbnorm.sh --help 469s 469s Written by Brian Bushnell 469s Last modified October 19, 2017 469s 469s Description: Normalizes read depth based on kmer counts. 469s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 469s However, Tadpole has superior error-correction to BBNorm. 469s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 469s 469s Usage: bbnorm.sh in= out= outt= hist= 469s 469s Input parameters: 469s in=null Primary input. Use in2 for paired reads in a second file 469s in2=null Second input file for paired reads in two files 469s extra=null Additional files to use for input (generating hash table) but not for output 469s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 469s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 469s kmersample=1 Process every nth kmer, and skip the rest 469s readsample=1 Process every nth read, and skip the rest 469s interleaved=auto May be set to true or false to force the input read file to ovverride autodetection of the input file as paired interleaved. 469s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 469s 469s Output parameters: 469s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 469s outt= (outtoss) File for reads that were excluded from primary output 469s reads=-1 Only process this number of reads, then quit (-1 means all) 469s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 469s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 469s zerobin=f Set to true if you want kmers with a count of 0 to go in the 0 bin instead of the 1 bin in histograms. 469s Default is false, to prevent confusion about how there can be 0-count kmers. 469s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 469s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 469s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 469s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 469s rename=f Rename reads based on their kmer depth. 469s 469s Hashing parameters: 469s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 469s bits=32 Bits per cell in bloom filter; must be 2, 4, 8, 16, or 32. Maximum kmer depth recorded is 2^cbits. Automatically reduced to 16 in 2-pass. 469s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 469s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 469s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 469s prefilter=f True is slower, but generally more accurate; filters out low-depth kmers from the main hashtable. The prefilter is more memory-efficient because it uses 2-bit cells. 469s prehashes=2 Number of hashes for prefilter. 469s prefilterbits=2 (pbits) Bits per cell in prefilter. 469s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 469s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 469s minq=6 Ignore kmers containing bases with quality below this 469s minprob=0.5 Ignore kmers with overall probability of correctness below this 469s threads=auto (t) Spawn exactly X hashing threads (default is number of logical processors). Total active threads may exceed X due to I/O threads. 469s rdk=t (removeduplicatekmers) When true, a kmer's count will only be incremented once per read pair, even if that kmer occurs more than once. 469s 469s Normalization parameters: 469s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 469s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 469s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 469s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 469s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 469s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 469s percentile=54.0 (dp) Read depth is by default inferred from the 54th percentile of kmer depth, but this may be changed to any number 1-100. 469s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 469s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 469s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 469s 469s Error detection parameters: 469s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 469s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 469s tossbadreads=f (tbr) Throw away reads detected as containing errors. 469s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 469s errordetectratio=125 (edr) Reads with a ratio of at least this much between their high and low depth kmers will be classified as error reads. 469s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 469s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 469s 469s Error correction parameters: 469s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 469s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 469s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 469s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 469s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 469s eccmaxqual=127 Do not correct bases with quality above this value. 469s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 469s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 469s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 469s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 469s overlap=f (ecco) Error correct by read overlap. 469s 469s Depth binning parameters: 469s lowbindepth=10 (lbd) Cutoff for low depth bin. 469s highbindepth=80 (hbd) Cutoff for high depth bin. 469s outlow= Pairs in which both reads have a median below lbd go into this file. 469s outhigh= Pairs in which both reads have a median above hbd go into this file. 469s outmid= All other pairs go into this file. 469s 469s Histogram parameters: 469s hist= Specify a file to write the input kmer depth histogram. 469s histout= Specify a file to write the output kmer depth histogram. 469s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 469s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 469s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 469s 469s Peak calling parameters: 469s peaks= Write the peaks to this file. Default is stdout. 469s minHeight=2 (h) Ignore peaks shorter than this. 469s minVolume=5 (v) Ignore peaks with less area than this. 469s minWidth=3 (w) Ignore peaks narrower than this. 469s minPeak=2 (minp) Ignore peaks with an X-value below this. 469s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 469s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 469s 469s Java Parameters: 469s -Xmx This will set Java's memory usage, overriding autodetection. 469s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 469s The max is typically 85% of physical memory. 469s -eoom This flag will cause the process to exit if an 469s out-of-memory exception occurs. Requires Java 8u92+. 469s -da Disable assertions. 469s 469s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 469s 469s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 469s out=out3.fastq outt=outt.fastq hist=hist.plt 469s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 469s java -ea -Xmx2635m -Xms2635m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 in=sanger_full_range_original_sanger.fastq qin=33 out=out3.fastq outt=outt.fastq hist=hist.plt 469s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 469s 469s 469s *********** Pass 1 ********** 469s 469s 469s Settings: 469s threads: 4 469s k: 31 469s deterministic: true 469s toss error reads: false 469s passes: 1 469s bits per cell: 16 469s cells: 980.97M 469s hashes: 3 469s base min quality: 5 469s kmer min prob: 0.5 469s 469s target depth: 400 469s min depth: 3 469s max depth: 500 469s min good kmers: 15 469s depth percentile: 64.8 469s ignore dupe kmers: true 469s fix spikes: false 469s histogram length: 65536 469s print zero cov: false 469s 472s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 472s 472s Estimated unique kmers: 7 472s 472s Table creation time: 2.753 seconds. 472s Started output threads. 472s Started output threads. 472s Table read time: 0.008 seconds. 23.58 kb/sec 472s Total reads in: 2 0.000% Kept 472s Total bases in: 188 0.000% Kept 472s Error reads in: 2 100.000% 472s Error type 1: 2 100.000% 472s Error type 2: 0 0.000% 472s Error type 3: 0 0.000% 472s 472s Wrote histogram to hist.plt 472s Total kmers counted: 128 472s Total unique kmer count: 128 472s Includes forward kmers only. 472s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 472s The most accurate value is the greater of the two. 472s 472s Percent unique: 100.00% 472s Depth average: 1.00 (unique kmers) 472s Depth median: 1 (unique kmers) 472s Depth standard deviation: 0.00 (unique kmers) 472s Corrected depth average: 0.00 472s 472s Depth average: 1.00 (all kmers) 472s Depth median: 1 (all kmers) 472s Depth standard deviation: 0.00 (all kmers) 472s 472s Approx. read depth median: 1.47 472s 472s *********** Pass 2 ********** 472s 472s 472s Settings: 472s threads: 4 472s k: 31 472s deterministic: true 472s toss error reads: false 472s passes: 1 472s bits per cell: 16 472s cells: 980.97M 472s hashes: 3 472s base min quality: 5 472s kmer min prob: 0.5 472s 472s target depth: 100 472s min depth: 5 472s max depth: 100 472s min good kmers: 15 472s depth percentile: 54.0 472s ignore dupe kmers: true 472s fix spikes: false 472s histogram length: 65536 472s 474s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 474s 474s Estimated unique kmers: 0 474s 474s Table creation time: 2.585 seconds. 474s Started output threads. 474s Started output threads. 474s Table read time: 0.002 seconds. 0.00 kb/sec 474s Total reads in: 0 NaN% Kept 474s Total bases in: 0 NaN% Kept 474s Error reads in: 0 NaN% 474s Error type 1: 0 NaN% 474s Error type 2: 0 NaN% 474s Error type 3: 0 NaN% 474s Total kmers counted: 0 474s Total unique kmer count: 0 474s Includes forward kmers only. 474s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 474s The most accurate value is the greater of the two. 474s 474s Percent unique: NaN% 474s Depth average: NaN (unique kmers) 474s Depth median: 0 (unique kmers) 474s Depth standard deviation: NaN (unique kmers) 474s Corrected depth average: NaN 474s 474s Depth average: NaN (all kmers) 474s Depth median: 0 (all kmers) 474s Depth standard deviation: 0.00 (all kmers) 474s 474s Approx. read depth median: NaN 474s 474s Removing temp files. 474s 474s Total time: 5.459 seconds. 0.03 kb/sec 474s test -r out3.fastq 474s test -r outt.fastq 474s test -r hist.plt 474s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 474s out=out4.fastq outt=outt2.fastq hist=hist2.plt 474s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 474s java -ea -Xmx2636m -Xms2636m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 in=illumina_full_range_original_illumina.fastq qin=64 out=out4.fastq outt=outt2.fastq hist=hist2.plt 475s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 475s 475s 475s *********** Pass 1 ********** 475s 475s 475s Settings: 475s threads: 4 475s k: 31 475s deterministic: true 475s toss error reads: false 475s passes: 1 475s bits per cell: 16 475s cells: 980.97M 475s hashes: 3 475s base min quality: 5 475s kmer min prob: 0.5 475s 475s target depth: 400 475s min depth: 3 475s max depth: 500 475s min good kmers: 15 475s depth percentile: 64.8 475s ignore dupe kmers: true 475s fix spikes: false 475s histogram length: 65536 475s print zero cov: false 475s 477s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 477s 477s Estimated unique kmers: 7 477s 477s Table creation time: 2.721 seconds. 477s Started output threads. 477s Started output threads. 477s Table read time: 0.007 seconds. 18.86 kb/sec 477s Total reads in: 2 0.000% Kept 477s Total bases in: 126 0.000% Kept 477s Error reads in: 2 100.000% 477s Error type 1: 2 100.000% 477s Error type 2: 0 0.000% 477s Error type 3: 0 0.000% 477s 477s Wrote histogram to hist2.plt 477s Total kmers counted: 66 477s Total unique kmer count: 66 477s Includes forward kmers only. 477s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 477s The most accurate value is the greater of the two. 477s 477s Percent unique: 100.00% 477s Depth average: 1.00 (unique kmers) 477s Depth median: 1 (unique kmers) 477s Depth standard deviation: 0.00 (unique kmers) 477s Corrected depth average: 0.00 477s 477s Depth average: 1.00 (all kmers) 477s Depth median: 1 (all kmers) 477s Depth standard deviation: 0.00 (all kmers) 477s 477s Approx. read depth median: 1.91 477s 477s *********** Pass 2 ********** 477s 477s 477s Settings: 477s threads: 4 477s k: 31 477s deterministic: true 477s toss error reads: false 477s passes: 1 477s bits per cell: 16 477s cells: 980.97M 477s hashes: 3 477s base min quality: 5 477s kmer min prob: 0.5 477s 477s target depth: 100 477s min depth: 5 477s max depth: 100 477s min good kmers: 15 477s depth percentile: 54.0 477s ignore dupe kmers: true 477s fix spikes: false 477s histogram length: 65536 477s 480s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 480s 480s Estimated unique kmers: 0 480s 480s Table creation time: 2.563 seconds. 480s Started output threads. 480s Started output threads. 480s Table read time: 0.002 seconds. 0.00 kb/sec 480s Total reads in: 0 NaN% Kept 480s Total bases in: 0 NaN% Kept 480s Error reads in: 0 NaN% 480s Error type 1: 0 NaN% 480s Error type 2: 0 NaN% 480s Error type 3: 0 NaN% 480s Total kmers counted: 0 480s Total unique kmer count: 0 480s Includes forward kmers only. 480s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 480s The most accurate value is the greater of the two. 480s 480s Percent unique: NaN% 480s Depth average: NaN (unique kmers) 480s Depth median: 0 (unique kmers) 480s Depth standard deviation: NaN (unique kmers) 480s Corrected depth average: NaN 480s 480s Depth average: NaN (all kmers) 480s Depth median: 0 (all kmers) 480s Depth standard deviation: 0.00 (all kmers) 480s 480s Approx. read depth median: NaN 480s 480s Removing temp files. 480s 480s Total time: 5.410 seconds. 0.02 kb/sec 480s test -r out4.fastq 480s test -r outt2.fastq 480s test -r hist2.plt 480s autopkgtest [07:56:46]: test run-unit-test: -----------------------] 481s autopkgtest [07:56:47]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 481s run-unit-test PASS 481s autopkgtest [07:56:47]: @@@@@@@@@@@@@@@@@@@@ summary 481s run-unit-test PASS 501s Creating nova instance adt-noble-ppc64el-bbmap-20240321-074846-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240321.img (UUID f9947641-425a-45c2-937a-6db4500fbfac)...