0s autopkgtest [17:15:55]: starting date and time: 2024-03-21 17:15:55+0000 0s autopkgtest [17:15:55]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:15:55]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.20_9mu1i/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-8,src:alsa-lib,src:libpng1.6,src:wp2latex --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-8/8u402-ga-2ubuntu6 alsa-lib/1.2.11-1build1 libpng1.6/1.6.43-3 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-3@bos02-s390x-9.secgroup --name adt-noble-s390x-bbmap-20240321-171555-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 98s autopkgtest [17:17:33]: testbed dpkg architecture: s390x 98s autopkgtest [17:17:33]: testbed apt version: 2.7.12 98s autopkgtest [17:17:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup 100s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 100s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 100s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3758 kB] 102s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 103s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 103s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [663 kB] 103s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 103s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 103s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 103s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3981 kB] 104s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 104s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [45.1 kB] 104s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 107s Fetched 9131 kB in 6s (1555 kB/s) 108s Reading package lists... 112s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s Calculating upgrade... 114s The following packages will be upgraded: 114s debianutils 114s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s Need to get 90.1 kB of archives. 114s After this operation, 1024 B of additional disk space will be used. 114s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x debianutils s390x 5.17 [90.1 kB] 115s Fetched 90.1 kB in 0s (206 kB/s) 115s (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 ... 52171 files and directories currently installed.) 115s Preparing to unpack .../debianutils_5.17_s390x.deb ... 115s Unpacking debianutils (5.17) over (5.16) ... 115s Setting up debianutils (5.17) ... 116s Processing triggers for man-db (2.12.0-3) ... 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Unknown architecture, assuming PC-style ttyS0 119s sh: Attempting to set up Debian/Ubuntu apt sources automatically 120s sh: Distribution appears to be Ubuntu 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s eatmydata is already the newest version (131-1). 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Reading package lists... 123s Building dependency tree... 123s Reading state information... 123s dbus is already the newest version (1.14.10-4ubuntu1). 123s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 123s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s rng-tools-debian is already the newest version (2.4). 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s The following packages will be REMOVED: 125s cloud-init* python3-configobj* python3-debconf* 126s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 126s After this operation, 3252 kB disk space will be freed. 126s (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 ... 52171 files and directories currently installed.) 126s Removing cloud-init (24.1.1-0ubuntu1) ... 127s Removing python3-configobj (5.0.8-3) ... 127s Removing python3-debconf (1.5.86) ... 127s Processing triggers for man-db (2.12.0-3) ... 128s (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 ... 51782 files and directories currently installed.) 128s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 129s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 129s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 129s invoke-rc.d: policy-rc.d denied execution of try-restart. 129s Reading package lists... 130s Building dependency tree... 130s Reading state information... 130s linux-generic is already the newest version (6.8.0-11.11+1). 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 131s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 131s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 134s Reading package lists... 134s Reading package lists... 135s Building dependency tree... 135s Reading state information... 135s Calculating upgrade... 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 137s autopkgtest [17:18:12]: rebooting testbed after setup commands that affected boot 163s autopkgtest [17:18:38]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 166s autopkgtest [17:18:41]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 170s Get:1 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (dsc) [2286 B] 170s Get:2 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (tar) [5343 kB] 170s Get:3 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (diff) [25.4 kB] 170s gpgv: Signature made Fri Nov 24 11:00:29 2023 UTC 170s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 170s gpgv: issuer "emollier@debian.org" 170s gpgv: Can't check signature: No public key 170s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.06+dfsg-1.dsc: no acceptable signature found 172s autopkgtest [17:18:47]: testing package bbmap version 39.06+dfsg-1 172s autopkgtest [17:18:47]: build not needed 173s autopkgtest [17:18:48]: test run-unit-test: preparing testbed 177s Reading package lists... 177s Building dependency tree... 177s Reading state information... 178s Starting pkgProblemResolver with broken count: 0 178s Starting 2 pkgProblemResolver with broken count: 0 178s Done 178s The following additional packages will be installed: 178s bbmap bbmap-jni ca-certificates-java fontconfig-config fonts-dejavu-core 178s fonts-dejavu-mono java-common libapache-pom-java libasound2 libasound2-data 178s libavahi-client3 libavahi-common-data libavahi-common3 libcommons-cli-java 178s libcommons-codec-java libcommons-io-java libcommons-parent-java libcups2 178s libfontconfig1 libfreetype6 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 178s libjpeg8 liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 178s openjdk-17-jre-headless python-biopython-doc 178s Suggested packages: 178s default-jre libasound2-plugins alsa-utils libcommons-io-java-doc cups-common 178s liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd libnss-mdns 178s fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 178s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 178s Recommended packages: 178s pigz alsa-ucm-conf alsa-topology-conf python3-biopython 178s The following NEW packages will be installed: 178s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java fontconfig-config 178s fonts-dejavu-core fonts-dejavu-mono java-common libapache-pom-java 178s libasound2 libasound2-data libavahi-client3 libavahi-common-data 178s libavahi-common3 libcommons-cli-java libcommons-codec-java 178s libcommons-io-java libcommons-parent-java libcups2 libfontconfig1 178s libfreetype6 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 liblcms2-2 178s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 178s python-biopython-doc 179s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 179s Need to get 78.1 MB/78.1 MB of archives. 179s After this operation, 226 MB of additional disk space will be used. 179s Get:1 /tmp/autopkgtest.W1idzj/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [720 B] 179s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-cli-java all 1.6.0-1 [59.9 kB] 179s Get:3 http://ftpmaster.internal/ubuntu noble/universe s390x libapache-pom-java all 29-2 [5284 B] 179s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-parent-java all 56-1 [10.7 kB] 179s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-codec-java all 1.16.0-1 [306 kB] 179s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-io-java all 2.11.0-2 [297 kB] 179s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x liblog4j1.2-java all 1.2.17-11 [439 kB] 179s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x libmpj-java all 0.44+dfsg-4 [443 kB] 179s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x ca-certificates-java all 20240118 [11.6 kB] 179s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x java-common all 0.75+exp1 [6798 B] 179s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libavahi-common-data s390x 0.8-13ubuntu2 [29.5 kB] 179s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libavahi-common3 s390x 0.8-13ubuntu2 [23.8 kB] 179s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libavahi-client3 s390x 0.8-13ubuntu2 [26.7 kB] 179s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libcups2 s390x 2.4.6-0ubuntu3 [277 kB] 179s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x liblcms2-2 s390x 2.14-2 [155 kB] 179s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB] 179s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 179s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libfreetype6 s390x 2.13.2+dfsg-1 [431 kB] 179s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 179s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 179s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig-config s390x 2.15.0-1ubuntu1 [37.0 kB] 179s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libfontconfig1 s390x 2.15.0-1ubuntu1 [150 kB] 179s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libasound2-data all 1.2.10-3build1 [20.7 kB] 179s Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libasound2 s390x 1.2.10-3build1 [414 kB] 180s Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2 [90.4 kB] 180s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libharfbuzz0b s390x 8.3.0-2 [515 kB] 180s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libpcsclite1 s390x 2.0.0-1 [19.9 kB] 180s Get:28 http://ftpmaster.internal/ubuntu noble/main s390x openjdk-17-jre-headless s390x 17.0.10+7-1 [45.7 MB] 182s Get:29 http://ftpmaster.internal/ubuntu noble/universe s390x bbmap all 39.06+dfsg-1 [9768 kB] 182s Get:30 http://ftpmaster.internal/ubuntu noble/universe s390x bbmap-jni s390x 39.06+dfsg-1 [38.7 kB] 182s Get:31 http://ftpmaster.internal/ubuntu noble/universe s390x python-biopython-doc all 1.81+dfsg-3 [17.3 MB] 183s Fetched 78.1 MB in 4s (19.3 MB/s) 183s Selecting previously unselected package libcommons-cli-java. 183s (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 ... 51727 files and directories currently installed.) 183s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 183s Unpacking libcommons-cli-java (1.6.0-1) ... 184s Selecting previously unselected package libapache-pom-java. 184s Preparing to unpack .../01-libapache-pom-java_29-2_all.deb ... 184s Unpacking libapache-pom-java (29-2) ... 184s Selecting previously unselected package libcommons-parent-java. 184s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 184s Unpacking libcommons-parent-java (56-1) ... 184s Selecting previously unselected package libcommons-codec-java. 184s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 184s Unpacking libcommons-codec-java (1.16.0-1) ... 184s Selecting previously unselected package libcommons-io-java. 184s Preparing to unpack .../04-libcommons-io-java_2.11.0-2_all.deb ... 184s Unpacking libcommons-io-java (2.11.0-2) ... 184s Selecting previously unselected package liblog4j1.2-java. 184s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 184s Unpacking liblog4j1.2-java (1.2.17-11) ... 184s Selecting previously unselected package libmpj-java. 184s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 184s Unpacking libmpj-java (0.44+dfsg-4) ... 184s Selecting previously unselected package ca-certificates-java. 184s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 184s Unpacking ca-certificates-java (20240118) ... 184s Selecting previously unselected package java-common. 184s Preparing to unpack .../08-java-common_0.75+exp1_all.deb ... 184s Unpacking java-common (0.75+exp1) ... 184s Selecting previously unselected package libavahi-common-data:s390x. 184s Preparing to unpack .../09-libavahi-common-data_0.8-13ubuntu2_s390x.deb ... 184s Unpacking libavahi-common-data:s390x (0.8-13ubuntu2) ... 184s Selecting previously unselected package libavahi-common3:s390x. 184s Preparing to unpack .../10-libavahi-common3_0.8-13ubuntu2_s390x.deb ... 184s Unpacking libavahi-common3:s390x (0.8-13ubuntu2) ... 184s Selecting previously unselected package libavahi-client3:s390x. 184s Preparing to unpack .../11-libavahi-client3_0.8-13ubuntu2_s390x.deb ... 184s Unpacking libavahi-client3:s390x (0.8-13ubuntu2) ... 184s Selecting previously unselected package libcups2:s390x. 184s Preparing to unpack .../12-libcups2_2.4.6-0ubuntu3_s390x.deb ... 184s Unpacking libcups2:s390x (2.4.6-0ubuntu3) ... 184s Selecting previously unselected package liblcms2-2:s390x. 184s Preparing to unpack .../13-liblcms2-2_2.14-2_s390x.deb ... 184s Unpacking liblcms2-2:s390x (2.14-2) ... 184s Selecting previously unselected package libjpeg-turbo8:s390x. 184s Preparing to unpack .../14-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ... 184s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 184s Selecting previously unselected package libjpeg8:s390x. 184s Preparing to unpack .../15-libjpeg8_8c-2ubuntu11_s390x.deb ... 184s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 184s Selecting previously unselected package libfreetype6:s390x. 184s Preparing to unpack .../16-libfreetype6_2.13.2+dfsg-1_s390x.deb ... 184s Unpacking libfreetype6:s390x (2.13.2+dfsg-1) ... 184s Selecting previously unselected package fonts-dejavu-mono. 184s Preparing to unpack .../17-fonts-dejavu-mono_2.37-8_all.deb ... 184s Unpacking fonts-dejavu-mono (2.37-8) ... 185s Selecting previously unselected package fonts-dejavu-core. 185s Preparing to unpack .../18-fonts-dejavu-core_2.37-8_all.deb ... 185s Unpacking fonts-dejavu-core (2.37-8) ... 185s Selecting previously unselected package fontconfig-config. 185s Preparing to unpack .../19-fontconfig-config_2.15.0-1ubuntu1_s390x.deb ... 185s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 185s Selecting previously unselected package libfontconfig1:s390x. 185s Preparing to unpack .../20-libfontconfig1_2.15.0-1ubuntu1_s390x.deb ... 185s Unpacking libfontconfig1:s390x (2.15.0-1ubuntu1) ... 185s Selecting previously unselected package libasound2-data. 185s Preparing to unpack .../21-libasound2-data_1.2.10-3build1_all.deb ... 185s Unpacking libasound2-data (1.2.10-3build1) ... 185s Selecting previously unselected package libasound2:s390x. 185s Preparing to unpack .../22-libasound2_1.2.10-3build1_s390x.deb ... 185s Unpacking libasound2:s390x (1.2.10-3build1) ... 186s Selecting previously unselected package libgraphite2-3:s390x. 186s Preparing to unpack .../23-libgraphite2-3_1.3.14-2_s390x.deb ... 186s Unpacking libgraphite2-3:s390x (1.3.14-2) ... 186s Selecting previously unselected package libharfbuzz0b:s390x. 186s Preparing to unpack .../24-libharfbuzz0b_8.3.0-2_s390x.deb ... 186s Unpacking libharfbuzz0b:s390x (8.3.0-2) ... 186s Selecting previously unselected package libpcsclite1:s390x. 186s Preparing to unpack .../25-libpcsclite1_2.0.0-1_s390x.deb ... 186s Unpacking libpcsclite1:s390x (2.0.0-1) ... 186s Selecting previously unselected package openjdk-17-jre-headless:s390x. 186s Preparing to unpack .../26-openjdk-17-jre-headless_17.0.10+7-1_s390x.deb ... 186s Unpacking openjdk-17-jre-headless:s390x (17.0.10+7-1) ... 189s Selecting previously unselected package bbmap. 189s Preparing to unpack .../27-bbmap_39.06+dfsg-1_all.deb ... 189s Unpacking bbmap (39.06+dfsg-1) ... 190s Selecting previously unselected package bbmap-jni. 190s Preparing to unpack .../28-bbmap-jni_39.06+dfsg-1_s390x.deb ... 190s Unpacking bbmap-jni (39.06+dfsg-1) ... 190s Selecting previously unselected package python-biopython-doc. 190s Preparing to unpack .../29-python-biopython-doc_1.81+dfsg-3_all.deb ... 190s Unpacking python-biopython-doc (1.81+dfsg-3) ... 190s Selecting previously unselected package autopkgtest-satdep. 190s Preparing to unpack .../30-1-autopkgtest-satdep.deb ... 190s Unpacking autopkgtest-satdep (0) ... 190s Setting up libgraphite2-3:s390x (1.3.14-2) ... 190s Setting up liblcms2-2:s390x (2.14-2) ... 190s Setting up java-common (0.75+exp1) ... 190s Setting up libcommons-cli-java (1.6.0-1) ... 190s Setting up liblog4j1.2-java (1.2.17-11) ... 190s Setting up libasound2-data (1.2.10-3build1) ... 190s Setting up libfreetype6:s390x (2.13.2+dfsg-1) ... 190s Setting up libapache-pom-java (29-2) ... 190s Setting up libavahi-common-data:s390x (0.8-13ubuntu2) ... 190s Setting up fonts-dejavu-mono (2.37-8) ... 190s Setting up fonts-dejavu-core (2.37-8) ... 190s Setting up libpcsclite1:s390x (2.0.0-1) ... 190s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 190s Setting up python-biopython-doc (1.81+dfsg-3) ... 190s Setting up libasound2:s390x (1.2.10-3build1) ... 190s Setting up libharfbuzz0b:s390x (8.3.0-2) ... 190s Setting up bbmap-jni (39.06+dfsg-1) ... 190s Setting up ca-certificates-java (20240118) ... 190s No JRE found. Skipping Java certificates setup. 190s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 190s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 191s Setting up libcommons-parent-java (56-1) ... 191s Setting up libavahi-common3:s390x (0.8-13ubuntu2) ... 191s Setting up libfontconfig1:s390x (2.15.0-1ubuntu1) ... 191s Setting up libcommons-codec-java (1.16.0-1) ... 191s Setting up libavahi-client3:s390x (0.8-13ubuntu2) ... 191s Setting up libcommons-io-java (2.11.0-2) ... 191s Setting up libmpj-java (0.44+dfsg-4) ... 191s Setting up libcups2:s390x (2.4.6-0ubuntu3) ... 191s Setting up openjdk-17-jre-headless:s390x (17.0.10+7-1) ... 191s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/java to provide /usr/bin/java (java) in auto mode 191s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 191s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 191s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 191s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 191s Processing triggers for libc-bin (2.39-0ubuntu2) ... 191s Processing triggers for man-db (2.12.0-3) ... 192s Processing triggers for ca-certificates-java (20240118) ... 193s Adding debian:ACCVRAIZ1.pem 193s Adding debian:AC_RAIZ_FNMT-RCM.pem 193s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 193s Adding debian:ANF_Secure_Server_Root_CA.pem 193s Adding debian:Actalis_Authentication_Root_CA.pem 193s Adding debian:AffirmTrust_Commercial.pem 193s Adding debian:AffirmTrust_Networking.pem 193s Adding debian:AffirmTrust_Premium.pem 193s Adding debian:AffirmTrust_Premium_ECC.pem 193s Adding debian:Amazon_Root_CA_1.pem 193s Adding debian:Amazon_Root_CA_2.pem 193s Adding debian:Amazon_Root_CA_3.pem 193s Adding debian:Amazon_Root_CA_4.pem 193s Adding debian:Atos_TrustedRoot_2011.pem 193s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 193s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 193s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 193s Adding debian:BJCA_Global_Root_CA1.pem 193s Adding debian:BJCA_Global_Root_CA2.pem 193s Adding debian:Baltimore_CyberTrust_Root.pem 193s Adding debian:Buypass_Class_2_Root_CA.pem 193s Adding debian:Buypass_Class_3_Root_CA.pem 193s Adding debian:CA_Disig_Root_R2.pem 193s Adding debian:CFCA_EV_ROOT.pem 193s Adding debian:COMODO_Certification_Authority.pem 193s Adding debian:COMODO_ECC_Certification_Authority.pem 193s Adding debian:COMODO_RSA_Certification_Authority.pem 193s Adding debian:Certainly_Root_E1.pem 193s Adding debian:Certainly_Root_R1.pem 193s Adding debian:Certigna.pem 193s Adding debian:Certigna_Root_CA.pem 193s Adding debian:Certum_EC-384_CA.pem 193s Adding debian:Certum_Trusted_Network_CA.pem 193s Adding debian:Certum_Trusted_Network_CA_2.pem 193s Adding debian:Certum_Trusted_Root_CA.pem 193s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 193s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 193s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 193s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 193s Adding debian:Comodo_AAA_Services_root.pem 193s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 193s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 193s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 193s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 193s Adding debian:DigiCert_Assured_ID_Root_CA.pem 193s Adding debian:DigiCert_Assured_ID_Root_G2.pem 193s Adding debian:DigiCert_Assured_ID_Root_G3.pem 193s Adding debian:DigiCert_Global_Root_CA.pem 193s Adding debian:DigiCert_Global_Root_G2.pem 193s Adding debian:DigiCert_Global_Root_G3.pem 193s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 193s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 193s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 193s Adding debian:DigiCert_Trusted_Root_G4.pem 193s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 193s Adding debian:Entrust_Root_Certification_Authority.pem 193s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 193s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 193s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 193s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 193s Adding debian:GLOBALTRUST_2020.pem 193s Adding debian:GTS_Root_R1.pem 193s Adding debian:GTS_Root_R2.pem 193s Adding debian:GTS_Root_R3.pem 193s Adding debian:GTS_Root_R4.pem 193s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 193s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 193s Adding debian:GlobalSign_Root_CA.pem 193s Adding debian:GlobalSign_Root_CA_-_R3.pem 193s Adding debian:GlobalSign_Root_CA_-_R6.pem 193s Adding debian:GlobalSign_Root_E46.pem 193s Adding debian:GlobalSign_Root_R46.pem 193s Adding debian:Go_Daddy_Class_2_CA.pem 193s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 193s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 193s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 193s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 193s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 193s Adding debian:HiPKI_Root_CA_-_G1.pem 193s Adding debian:Hongkong_Post_Root_CA_3.pem 193s Adding debian:ISRG_Root_X1.pem 193s Adding debian:ISRG_Root_X2.pem 193s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 193s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 193s Adding debian:Izenpe.com.pem 193s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 193s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 193s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 193s Adding debian:NAVER_Global_Root_Certification_Authority.pem 193s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 193s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 193s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 193s Adding debian:QuoVadis_Root_CA_1_G3.pem 193s Adding debian:QuoVadis_Root_CA_2.pem 193s Adding debian:QuoVadis_Root_CA_2_G3.pem 193s Adding debian:QuoVadis_Root_CA_3.pem 193s Adding debian:QuoVadis_Root_CA_3_G3.pem 193s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 193s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 193s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 193s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 193s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 193s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 193s Adding debian:SZAFIR_ROOT_CA2.pem 193s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 193s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 193s Adding debian:SecureSign_RootCA11.pem 193s Adding debian:SecureTrust_CA.pem 193s Adding debian:Secure_Global_CA.pem 193s Adding debian:Security_Communication_ECC_RootCA1.pem 193s Adding debian:Security_Communication_RootCA2.pem 193s Adding debian:Security_Communication_RootCA3.pem 193s Adding debian:Security_Communication_Root_CA.pem 193s Adding debian:Starfield_Class_2_CA.pem 193s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 193s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 193s Adding debian:SwissSign_Gold_CA_-_G2.pem 193s Adding debian:SwissSign_Silver_CA_-_G2.pem 193s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 193s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 193s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 193s Adding debian:TWCA_Global_Root_CA.pem 193s Adding debian:TWCA_Root_Certification_Authority.pem 193s Adding debian:TeliaSonera_Root_CA_v1.pem 193s Adding debian:Telia_Root_CA_v2.pem 193s Adding debian:TrustAsia_Global_Root_CA_G3.pem 193s Adding debian:TrustAsia_Global_Root_CA_G4.pem 193s Adding debian:Trustwave_Global_Certification_Authority.pem 193s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 193s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 193s Adding debian:TunTrust_Root_CA.pem 193s Adding debian:UCA_Extended_Validation_Root.pem 193s Adding debian:UCA_Global_G2_Root.pem 193s Adding debian:USERTrust_ECC_Certification_Authority.pem 193s Adding debian:USERTrust_RSA_Certification_Authority.pem 193s Adding debian:XRamp_Global_CA_Root.pem 193s Adding debian:certSIGN_ROOT_CA.pem 193s Adding debian:certSIGN_Root_CA_G2.pem 193s Adding debian:e-Szigno_Root_CA_2017.pem 193s Adding debian:ePKI_Root_Certification_Authority.pem 193s Adding debian:emSign_ECC_Root_CA_-_C3.pem 193s Adding debian:emSign_ECC_Root_CA_-_G3.pem 193s Adding debian:emSign_Root_CA_-_C1.pem 193s Adding debian:emSign_Root_CA_-_G1.pem 193s Adding debian:vTrus_ECC_Root_CA.pem 193s Adding debian:vTrus_Root_CA.pem 193s done. 193s Setting up bbmap (39.06+dfsg-1) ... 193s Setting up autopkgtest-satdep (0) ... 197s (Reading database ... 54569 files and directories currently installed.) 197s Removing autopkgtest-satdep (0) ... 198s autopkgtest [17:19:13]: test run-unit-test: [----------------------- 198s 198s # bbmap 198s bbmap.sh --version 198s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 198s java -ea -Xmx2844m -Xms2844m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 199s BBMap version 39.06 199s For help, please run the shellscript with no parameters, or look in /docs/. 199s bbmap.sh --help 199s 199s BBMap 199s Written by Brian Bushnell, from Dec. 2010 - present 199s Last modified September 15, 2022 199s 199s Description: Fast and accurate splice-aware read aligner. 199s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 199s 199s To index: bbmap.sh ref= 199s To map: bbmap.sh in= out= 199s To map without writing an index: 199s bbmap.sh ref= in= out= nodisk 199s 199s in=stdin will accept reads from standard in, and out=stdout will write to 199s standard out, but file extensions are still needed to specify the format of the 199s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 199s standard in; out=stdout.sam.gz will write gzipped sam. 199s 199s Indexing Parameters (required when building the index): 199s nodisk=f Set to true to build index in memory and write nothing 199s to disk except output. 199s ref= Specify the reference sequence. Only do this ONCE, 199s when building the index (unless using 'nodisk'). 199s build=1 If multiple references are indexed in the same directory, 199s each needs a unique numeric ID (unless using 'nodisk'). 199s k=13 Kmer length, range 8-15. Longer is faster but uses 199s more memory. Shorter is more sensitive. 199s If indexing and mapping are done in two steps, K should 199s be specified each time. 199s path=<.> Specify the location to write the index, if you don't 199s want it in the current working directory. 199s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 199s number (reduces RAM by 50% and sensitivity slightly). 199s Should be enabled both when building the index AND 199s when mapping. 199s rebuild=f Force a rebuild of the index (ref= should be set). 199s 199s Input Parameters: 199s build=1 Designate index to use. Corresponds to the number 199s specified when building the index. 199s in= Primary reads input; required parameter. 199s in2= For paired reads in two files. 199s interleaved=auto True forces paired/interleaved input; false forces 199s single-ended mapping. If not specified, interleaved 199s status will be autodetected from read names. 199s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 199s BBMap and 6000 for BBMapPacBio. Only works for FASTA 199s input (use 'maxlen' for FASTQ input). The default for 199s bbmap.sh is 500, and for mapPacBio.sh is 6000. 199s unpigz=f Spawn a pigz (parallel gzip) process for faster 199s decompression than using Java. 199s Requires pigz to be installed. 199s touppercase=t (tuc) Convert lowercase letters in reads to upper case 199s (otherwise they will not match the reference). 199s 199s Sampling Parameters: 199s 199s reads=-1 Set to a positive number N to only process the first N 199s reads (or pairs), then quit. -1 means use all reads. 199s samplerate=1 Set to a number from 0 to 1 to randomly select that 199s fraction of reads for mapping. 1 uses all reads. 199s skipreads=0 Set to a number N to skip the first N reads (or pairs), 199s then map the rest. 199s 199s Mapping Parameters: 199s fast=f This flag is a macro which sets other paramters to run 199s faster, at reduced sensitivity. Bad for RNA-seq. 199s slow=f This flag is a macro which sets other paramters to run 199s slower, at greater sensitivity. 'vslow' is even slower. 199s maxindel=16000 Don't look for indels longer than this. Lower is faster. 199s Set to >=100k for RNAseq with long introns like mammals. 199s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 199s By default these are not sought, but may be found anyway. 199s tipsearch=100 Look this far for read-end deletions with anchors 199s shorter than K, using brute force. 199s minid=0.76 Approximate minimum alignment identity to look for. 199s Higher is faster and less sensitive. 199s minhits=1 Minimum number of seed hits required for candidate sites. 199s Higher is faster. 199s local=f Set to true to use local, rather than global, alignments. 199s This will soft-clip ugly ends of poor alignments. 199s perfectmode=f Allow only perfect mappings when set to true (very fast). 199s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 199s N's in the reference) mappings. 199s threads=auto (t) Set to number of threads desired. By default, uses 199s all cores available. 199s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 199s multiple top-scoring mapping locations). 199s best (use the first best site) 199s toss (consider unmapped) 199s random (select one top-scoring site randomly) 199s all (retain all top-scoring sites) 199s samestrandpairs=f (ssp) Specify whether paired reads should map to the 199s same strand or opposite strands. 199s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 199s orientation. Set to false for long-mate-pair libraries. 199s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 199s insert size or orientation, the read with the lower 199s mapping quality is marked unmapped. 199s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 199s be sent to 'outu' but not 'outm'. 199s rcomp=f Reverse complement both reads prior to mapping (for LMP 199s outward-facing libraries). 199s rcompmate=f Reverse complement read2 prior to mapping. 199s pairlen=32000 Set max allowed distance between paired reads. 199s (insert size)=(pairlen)+(read1 length)+(read2 length) 199s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 199s greater than this. Lower is faster. 199s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 199s is faster. 199s averagepairdist=100 (apd) Initial average distance between paired reads. 199s Varies dynamically; does not need to be specified. 199s deterministic=f Run in deterministic mode. In this case it is good 199s to set averagepairdist. BBMap is deterministic 199s without this flag if using single-ended reads, 199s or run singlethreaded. 199s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 199s fraction of read length. Faster but less accurate. 199s bandwidth=0 (bw) Set the bandwidth directly. 199s fraction of read length. Faster but less accurate. 199s usejni=f (jni) Do alignments faster, in C code. Requires 199s compiling the C code; details are in /jni/README.txt. 199s maxsites2=800 Don't analyze (or print) more than this many alignments 199s per read. 199s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 199s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 199s will ignore the most common 3% of kmers. 199s greedy=t Use a greedy algorithm to discard the least-useful 199s kmers on a per-read basis. 199s kfilter=0 If positive, potential mapping sites must have at 199s least this many consecutive exact matches. 199s 199s 199s Quality and Trimming Parameters: 199s qin=auto Set to 33 or 64 to specify input quality value ASCII 199s offset. 33 is Sanger, 64 is old Solexa. 199s qout=auto Set to 33 or 64 to specify output quality value ASCII 199s offset (only if output format is fastq). 199s qtrim=f Quality-trim ends before mapping. Options are: 199s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 199s untrim=f Undo trimming after mapping. Untrimmed bases will be 199s soft-clipped in cigar strings. 199s trimq=6 Trim regions with average quality below this 199s (phred algorithm). 199s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 199s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 199s quality strings for fasta input reads. 199s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 199s out-of-range quality values. 199s usequality=t Use quality scores when determining which read kmers 199s to use as seeds. 199s minaveragequality=0 (maq) Do not map reads with average quality below this. 199s maqb=0 If positive, calculate maq from this many initial bases. 199s 199s Output Parameters: 199s out= Write all reads to this file. 199s outu= Write only unmapped reads to this file. Does not 199s include unmapped paired reads with a mapped mate. 199s outm= Write only mapped reads to this file. Includes 199s unmapped paired reads with a mapped mate. 199s mappedonly=f If true, treats 'out' like 'outm'. 199s bamscript= (bs) Write a shell script to that will turn 199s the sam output into a sorted, indexed bam file. 199s ordered=f Set to true to output reads in same order as input. 199s Slower and uses more memory. 199s overwrite=f (ow) Allow process to overwrite existing files. 199s secondary=f Print secondary alignments. 199s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 199s with score of at least this fraction of primary. 199s ssao=f (secondarysiteasambiguousonly) Only print secondary 199s alignments for ambiguously-mapped reads. 199s maxsites=5 Maximum number of total alignments to print per read. 199s Only relevant when secondary=t. 199s quickmatch=f Generate cigar strings more quickly. 199s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 199s assuming that the remainder is a comment or description. 199s ziplevel=2 (zl) Compression level for zip or gzip output. 199s pigz=f Spawn a pigz (parallel gzip) process for faster 199s compression than Java. Requires pigz to be installed. 199s machineout=f Set to true to output statistics in machine-friendly 199s 'key=value' format. 199s printunmappedcount=f Print the total number of unmapped reads and bases. 199s If input is paired, the number will be of pairs 199s for which both reads are unmapped. 199s showprogress=0 If positive, print a '.' every X reads. 199s showprogress2=0 If positive, print the number of seconds since the 199s last progress update (instead of a '.'). 199s renamebyinsert=f Renames reads based on their mapped insert size. 199s 199s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 199s bloom=f Use a Bloom filter to ignore reads not sharing kmers 199s with the reference. This uses more memory, but speeds 199s mapping when most reads don't match the reference. 199s bloomhashes=2 Number of hash functions. 199s bloomminhits=3 Number of consecutive hits to be considered matched. 199s bloomk=31 Bloom filter kmer length. 199s bloomserial=t Use the serialized Bloom filter for greater loading 199s speed, if available. If not, generate and write one. 199s 199s Post-Filtering Parameters: 199s idfilter=0 Independant of minid; sets exact minimum identity 199s allowed for alignments to be printed. Range 0 to 1. 199s subfilter=-1 Ban alignments with more than this many substitutions. 199s insfilter=-1 Ban alignments with more than this many insertions. 199s delfilter=-1 Ban alignments with more than this many deletions. 199s indelfilter=-1 Ban alignments with more than this many indels. 199s editfilter=-1 Ban alignments with more than this many edits. 199s inslenfilter=-1 Ban alignments with an insertion longer than this. 199s dellenfilter=-1 Ban alignments with a deletion longer than this. 199s nfilter=-1 Ban alignments with more than this many ns. This 199s includes nocall, noref, and off scaffold ends. 199s 199s Sam flags and settings: 199s noheader=f Disable generation of header lines. 199s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 199s with = and X, or 1.3 to use M. 199s saa=t (secondaryalignmentasterisks) Use asterisks instead of 199s bases for sam secondary alignments. 199s cigar=t Set to 'f' to skip generation of cigar strings (faster). 199s keepnames=f Keep original names of paired reads, rather than 199s ensuring both reads have the same name. 199s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 199s cigar strings for deletions of at least that length. 199s rgid= Set readgroup ID. All other readgroup fields 199s can be set similarly, with the flag rgXX= 199s If you set a readgroup flag to the word 'filename', 199s e.g. rgid=filename, the input file name will be used. 199s mdtag=f Write MD tags. 199s nhtag=f Write NH tags. 199s xmtag=f Write XM tags (may only work correctly with ambig=all). 199s amtag=f Write AM tags. 199s nmtag=f Write NM tags. 199s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 199s for RNAseq using firststrand, secondstrand, or 199s unstranded libraries. Needed by Cufflinks. 199s JGI mainly uses 'firststrand'. 199s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 199s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 199s prefixed by YL:Z: 199s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 199s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 199s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 199s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 199s boundstag=f Write a tag indicating whether either read in the pair 199s goes off the end of the reference, prefixed by XB:Z: 199s notags=f Turn off all optional tags. 199s 199s Histogram and statistics output parameters: 199s scafstats= Statistics on how many reads mapped to which scaffold. 199s refstats= Statistics on how many reads mapped to which reference 199s file; only for BBSplit. 199s sortscafs=t Sort scaffolds or references by read count. 199s bhist= Base composition histogram by position. 199s qhist= Quality histogram by position. 199s aqhist= Histogram of average read quality. 199s bqhist= Quality histogram designed for box plots. 199s lhist= Read length histogram. 199s ihist= Write histogram of insert sizes (for paired reads). 199s ehist= Errors-per-read histogram. 199s qahist= Quality accuracy histogram of error rates versus 199s quality score. 199s indelhist= Indel length histogram. 199s mhist= Histogram of match, sub, del, and ins rates by 199s read location. 199s gchist= Read GC content histogram. 199s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 199s gcpairs=t Use average GC of paired reads. 199s idhist= Histogram of read count versus percent identity. 199s idbins=100 Number idhist bins. Set to 'auto' to use read length. 199s statsfile=stderr Mapping statistics are printed here. 199s 199s Coverage output parameters (these may reduce speed and use more RAM): 199s covstats= Per-scaffold coverage info. 199s rpkm= Per-scaffold RPKM/FPKM counts. 199s covhist= Histogram of # occurrences of each depth level. 199s basecov= Coverage per base location. 199s bincov= Print binned coverage per location (one line per X bases). 199s covbinsize=1000 Set the binsize for binned coverage output. 199s nzo=t Only print scaffolds with nonzero coverage. 199s twocolumn=f Change to true to print only ID and Avg_fold instead of 199s all 6 columns to the 'out=' file. 199s 32bit=f Set to true if you need per-base coverage over 64k. 199s strandedcov=f Track coverage for plus and minus strand independently. 199s startcov=f Only track start positions of reads. 199s secondarycov=t Include coverage of secondary alignments. 199s physcov=f Calculate physical coverage for paired reads. 199s This includes the unsequenced bases. 199s delcoverage=t (delcov) Count bases covered by deletions as covered. 199s True is faster than false. 199s covk=0 If positive, calculate kmer coverage statistics. 199s 199s Java Parameters: 199s -Xmx This will set Java's memory usage, 199s overriding autodetection. 199s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 199s will specify 800 megs. The max is typically 85% of 199s physical memory. The human genome requires around 24g, 199s or 12g with the 'usemodulo' flag. The index uses 199s roughly 6 bytes per reference base. 199s -eoom This flag will cause the process to exit if an 199s out-of-memory exception occurs. Requires Java 8u92+. 199s -da Disable assertions. 199s 199s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 199s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 199s 199s bbmap.sh ref=example.fasta 199s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 199s java -ea -Xmx2844m -Xms2844m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 199s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 199s Version 39.06 199s 199s No output file. 199s Writing reference. 199s 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] 199s 199s Set genScaffoldInfo=true 199s Writing chunk 1 199s Set genome to 1 199s 199s Loaded Reference: 0.012 seconds. 199s Loading index for chunk 1-1, build 1 199s No index available; generating from reference genome: /tmp/autopkgtest.W1idzj/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 200s Indexing threads started for block 0-1 200s Indexing threads finished for block 0-1 201s Generated Index: 2.257 seconds. 201s No reads to process; quitting. 201s 201s Total time: 2.491 seconds. 202s test -d ref 202s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 202s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 202s java -ea -Xmx2844m -Xms2844m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 202s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 202s Version 39.06 202s 202s Retaining first best site only for ambiguous mappings. 202s Set genome to 1 202s 202s Loaded Reference: 0.035 seconds. 202s Loading index for chunk 1-1, build 1 203s Generated Index: 1.250 seconds. 214s Analyzed Index: 11.179 seconds. 214s Started output stream: 0.035 seconds. 215s Cleared Memory: 0.177 seconds. 215s Processing reads in single-ended mode. 215s Started read stream. 215s Started 4 mapping threads. 215s Detecting finished threads: 0, 1, 2, 3 215s 215s ------------------ Results ------------------ 215s 215s Genome: 1 215s Key Length: 13 215s Max Indel: 16000 215s Minimum Score Ratio: 0.56 215s Mapping Mode: normal 215s Reads Used: 4 (153 bases) 215s 215s Mapping: 0.253 seconds. 215s Reads/sec: 15.82 215s kBases/sec: 0.61 215s 215s 215s Read 1 data: pct reads num reads pct bases num bases 215s 215s mapped: 0.0000% 0 0.0000% 0 215s unambiguous: 0.0000% 0 0.0000% 0 215s ambiguous: 0.0000% 0 0.0000% 0 215s low-Q discards: 25.0000% 1 19.6078% 30 215s 215s perfect best site: 0.0000% 0 0.0000% 0 215s semiperfect site: 0.0000% 0 0.0000% 0 215s 215s Match Rate: NA NA NaN% 0 215s Error Rate: NaN% 0 NaN% 0 215s Sub Rate: NaN% 0 NaN% 0 215s Del Rate: NaN% 0 NaN% 0 215s Ins Rate: NaN% 0 NaN% 0 215s N Rate: NaN% 0 NaN% 0 215s 215s Total time: 13.101 seconds. 215s test -r out.sam 215s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 215s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 215s java -ea -Xmx2844m -Xms2844m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 215s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 215s Version 39.06 215s 215s Retaining first best site only for ambiguous mappings. 215s 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] 215s 215s Set genScaffoldInfo=true 215s Set genome to 1 215s 215s Loaded Reference: 0.003 seconds. 215s Loading index for chunk 1-1, build 1 216s Indexing threads started for block 0-1 216s Indexing threads finished for block 0-1 216s Generated Index: 0.682 seconds. 227s Analyzed Index: 11.011 seconds. 227s Started output stream: 0.037 seconds. 227s Cleared Memory: 0.128 seconds. 228s Processing reads in single-ended mode. 228s Started read stream. 228s Started 4 mapping threads. 228s Detecting finished threads: 0, 1, 2, 3 228s 228s ------------------ Results ------------------ 228s 228s Genome: 1 228s Key Length: 13 228s Max Indel: 16000 228s Minimum Score Ratio: 0.56 228s Mapping Mode: normal 228s Reads Used: 3 (75 bases) 228s 228s Mapping: 0.188 seconds. 228s Reads/sec: 15.92 228s kBases/sec: 0.40 228s 228s 228s Read 1 data: pct reads num reads pct bases num bases 228s 228s mapped: 100.0000% 3 100.0000% 75 228s unambiguous: 100.0000% 3 100.0000% 75 228s ambiguous: 0.0000% 0 0.0000% 0 228s low-Q discards: 0.0000% 0 0.0000% 0 228s 228s perfect best site: 100.0000% 3 100.0000% 75 228s semiperfect site: 100.0000% 3 100.0000% 75 228s 228s Match Rate: NA NA 100.0000% 75 228s Error Rate: 0.0000% 0 0.0000% 0 228s Sub Rate: 0.0000% 0 0.0000% 0 228s Del Rate: 0.0000% 0 0.0000% 0 228s Ins Rate: 0.0000% 0 0.0000% 0 228s N Rate: 0.0000% 0 0.0000% 0 228s 228s Total time: 12.283 seconds. 228s test -r out2.sam 228s 228s # bbduk 228s bbduk.sh --version 228s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 228s java -ea -Xmx1422m -Xms1422m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 228s BBMap version 39.06 228s For help, please run the shellscript with no parameters, or look in /docs/. 228s bbduk.sh --help 228s 228s Written by Brian Bushnell 228s Last modified November 9, 2023 228s 228s Description: Compares reads to the kmers in a reference dataset, optionally 228s allowing an edit distance. Splits the reads into two outputs - those that 228s match the reference, and those that don't. Can also trim (remove) the matching 228s parts of the reads rather than binning the reads. 228s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 228s 228s Usage: bbduk.sh in= out= ref= 228s 228s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 228s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 228s fasta input, set in=stdin.fa.gz 228s 228s Input parameters: 228s in= Main input. in=stdin.fq will pipe from stdin. 228s in2= Input for 2nd read of pairs in a different file. 228s ref= Comma-delimited list of reference files. 228s In addition to filenames, you may also use the keywords: 228s adapters, artifacts, phix, lambda, pjet, mtst, kapa 228s literal= Comma-delimited list of literal reference sequences. 228s touppercase=f (tuc) Change all bases upper-case. 228s interleaved=auto (int) t/f overrides interleaved autodetection. 228s Must be set mainually when streaming fastq input. 228s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 228s reads=-1 If positive, quit after processing X reads or pairs. 228s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 228s possible unambiguous copies. Intended for short motifs 228s or adapter barcodes, as time/memory use is exponential. 228s samplerate=1 Set lower to only process a fraction of input reads. 228s samref= Optional reference fasta for processing sam files. 228s 228s Output parameters: 228s out= (outnonmatch) Write reads here that do not contain 228s kmers matching the database. 'out=stdout.fq' will pipe 228s to standard out. 228s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 228s different file. 228s outm= (outmatch) Write reads here that fail filters. In default 228s kfilter mode, this means any read with a matching kmer. 228s In any mode, it also includes reads that fail filters such 228s as minlength, mingc, maxgc, entropy, etc. In other words, 228s it includes all reads that do not go to 'out'. 228s outm2= (outmatch2) Use this to write 2nd read of pairs to a 228s different file. 228s outs= (outsingle) Use this to write singleton reads whose mate 228s was trimmed shorter than minlen. 228s stats= Write statistics about which contamininants were detected. 228s refstats= Write statistics on a per-reference-file basis. 228s rpkm= Write RPKM for each reference sequence (for RNA-seq). 228s dump= Dump kmer tables to a file, in fasta format. 228s duk= Write statistics in duk's format. *DEPRECATED* 228s nzo=t Only write statistics about ref sequences with nonzero hits. 228s overwrite=t (ow) Grant permission to overwrite files. 228s showspeed=t (ss) 'f' suppresses display of processing speed. 228s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 228s fastawrap=70 Length of lines in fasta output. 228s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 228s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 228s 5 includes base counts. 228s rename=f Rename reads to indicate which sequences they matched. 228s refnames=f Use names of reference files rather than scaffold IDs. 228s trd=f Truncate read and ref names at the first whitespace. 228s ordered=f Set to true to output reads in same order as input. 228s maxbasesout=-1 If positive, quit after writing approximately this many 228s bases to out (outu/outnonmatch). 228s maxbasesoutm=-1 If positive, quit after writing approximately this many 228s bases to outm (outmatch). 228s json=f Print to screen in json format. 228s 228s Histogram output parameters: 228s bhist= Base composition histogram by position. 228s qhist= Quality histogram by position. 228s qchist= Count of bases with each quality value. 228s aqhist= Histogram of average read quality. 228s bqhist= Quality histogram designed for box plots. 228s lhist= Read length histogram. 228s phist= Polymer length histogram. 228s gchist= Read GC content histogram. 228s enthist= Read entropy histogram. 228s ihist= Insert size histogram, for paired reads in mapped sam. 228s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 228s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 228s more memory. The default is 6000 for some histograms 228s and 80000 for others. 228s 228s Histograms for mapped sam/bam files only: 228s histbefore=t Calculate histograms from reads before processing. 228s ehist= Errors-per-read histogram. 228s qahist= Quality accuracy histogram of error rates versus quality 228s score. 228s indelhist= Indel length histogram. 228s mhist= Histogram of match, sub, del, and ins rates by position. 228s idhist= Histogram of read count versus percent identity. 228s idbins=100 Number idhist bins. Set to 'auto' to use read length. 228s varfile= Ignore substitution errors listed in this file when 228s calculating error rates. Can be generated with 228s CallVariants. 228s vcf= Ignore substitution errors listed in this VCF file 228s when calculating error rates. 228s ignorevcfindels=t Also ignore indels listed in the VCF. 228s 228s Processing parameters: 228s k=27 Kmer length used for finding contaminants. Contaminants 228s shorter than k will not be found. k must be at least 1. 228s rcomp=t Look for reverse-complements of kmers in addition to 228s forward kmers. 228s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 228s increase sensitivity in the presence of errors. This may 228s also be set to a number, e.g. mm=3, to mask that many bp. 228s The default mm=t corresponds to mm=1 for odd-length kmers 228s and mm=2 for even-length kmers (as of v39.04), while 228s mm=f is always equivalent to mm=0. 228s minkmerhits=1 (mkh) Reads need at least this many matching kmers 228s to be considered as matching the reference. 228s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 228s kmers to hit a ref, in order to be considered a match. 228s If this and minkmerhits are set, the greater is used. 228s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 228s bases to be covered by ref kmers to be considered a match. 228s If specified, mcf overrides mkh and mkf. 228s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 228s Memory use is proportional to (3*K)^hdist. 228s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 228s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 228s and indels). Memory use is proportional to (8*K)^edist. 228s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 228s qhdist2=0 Sets qhdist for short kmers, when using mink. 228s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 228s forbidn=f (fn) Forbids matching of read kmers containing N. 228s By default, these will match a reference 'A' if 228s hdist>0 or edist>0, to increase sensitivity. 228s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 228s match (or either is trimmed shorter than minlen). 228s Set to false to require both. 228s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 228s This makes the statistics a bit odd. 228s findbestmatch=f (fbm) If multiple matches, associate read with sequence 228s sharing most kmers. Reduces speed. 228s skipr1=f Don't do kmer-based operations on read 1. 228s skipr2=f Don't do kmer-based operations on read 2. 228s ecco=f For overlapping paired reads only. Performs error- 228s correction with BBMerge prior to kmer operations. 228s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 228s matrices generated by CalcTrueQuality. 228s sam= If recalibration is desired, and matrices have not already 228s been generated, BBDuk will create them from the sam file. 228s amino=f Run in amino acid mode. Some features have not been 228s tested, but kmer-matching works fine. Maximum k is 12. 228s 228s Speed and Memory parameters: 228s threads=auto (t) Set number of threads to use; default is number of 228s logical processors. 228s prealloc=f Preallocate memory in table. Allows faster table loading 228s and more efficient memory usage, for a large reference. 228s monitor=f Kill this process if it crashes. monitor=600,0.01 would 228s kill after 600 seconds under 1% usage. 228s minrskip=1 (mns) Force minimal skip interval when indexing reference 228s kmers. 1 means use all, 2 means use every other kmer, etc. 228s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 228s reference kmers. Normally all are used for scaffolds<100kb, 228s but with longer scaffolds, up to maxrskip-1 are skipped. 228s rskip= Set both minrskip and maxrskip to the same value. 228s If not set, rskip will vary based on sequence length. 228s qskip=1 Skip query kmers to increase speed. 1 means use all. 228s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 228s reads and reference. Increases speed and reduces memory. 228s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 228s 228s Trimming/Filtering/Masking parameters: 228s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 228s All kmer processing modes are mutually exclusive. 228s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 228s 228s ktrim=f Trim reads to remove bases matching reference kmers, plus 228s all bases to the left or right. 228s Values: 228s f (don't trim), 228s r (trim to the right), 228s l (trim to the left) 228s ktrimtips=0 Set this to a positive number to perform ktrim on both 228s ends, examining only the outermost X bases. 228s kmask= Replace bases matching ref kmers with another symbol. 228s Allows any non-whitespace character, and processes short 228s kmers on both ends if mink is set. 'kmask=lc' will 228s convert masked bases to lowercase. 228s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 228s ksplit=f For single-ended reads only. Reads will be split into 228s pairs around the kmer. If the kmer is at the end of the 228s read, it will be trimmed instead. Singletons will go to 228s out, and pairs will go to outm. Do not use ksplit with 228s other operations such as quality-trimming or filtering. 228s mink=0 Look for shorter kmers at read tips down to this length, 228s when k-trimming or masking. 0 means disabled. Enabling 228s this will disable maskmiddle. 228s qtrim=f Trim read ends to remove bases with quality below trimq. 228s Performed AFTER looking for kmers. Values: 228s rl (trim both ends), 228s f (neither end), 228s r (right end only), 228s l (left end only), 228s w (sliding window). 228s trimq=6 Regions with average quality BELOW this will be trimmed, 228s if qtrim is set to something other than f. Can be a 228s floating-point number like 7.3. 228s trimclip=f Trim soft-clipped bases from sam files. 228s minlength=10 (ml) Reads shorter than this after trimming will be 228s discarded. Pairs will be discarded if both are shorter. 228s mlf=0 (minlengthfraction) Reads shorter than this fraction of 228s original length after trimming will be discarded. 228s maxlength= Reads longer than this after trimming will be discarded. 228s minavgquality=0 (maq) Reads with average quality (after trimming) below 228s this will be discarded. 228s maqb=0 If positive, calculate maq from this many initial bases. 228s minbasequality=0 (mbq) Reads with any base below this quality (after 228s trimming) will be discarded. 228s maxns=-1 If non-negative, reads with more Ns than this 228s (after trimming) will be discarded. 228s mcb=0 (minconsecutivebases) Discard reads without at least 228s this many consecutive called bases. 228s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 228s than minlength to outm rather than discarding. 228s tp=0 (trimpad) Trim this much extra around matching kmers. 228s tbo=f (trimbyoverlap) Trim adapters based on where paired 228s reads overlap. 228s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 228s minoverlap=14 Require this many bases of overlap for detection. 228s mininsert=40 Require insert size of at least this for overlap. 228s Should be reduced to 16 for small RNA sequencing. 228s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 228s reads to the minimum length of either. 228s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 228s (exclusive, 0-based). 228s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 228s (exclusive, 0-based). 228s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 228s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 228s modulo this number. 228s restrictleft=0 If positive, only look for kmer matches in the 228s leftmost X bases. 228s restrictright=0 If positive, only look for kmer matches in the 228s rightmost X bases. 228s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 228s both ends is desired, use ktrimtips. 228s mingc=0 Discard reads with GC content below this. 228s maxgc=1 Discard reads with GC content above this. 228s gcpairs=t Use average GC of paired reads. 228s Also affects gchist. 228s tossjunk=f Discard reads with invalid characters as bases. 228s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 228s 228s Header-parsing parameters - these require Illumina headers: 228s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 228s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 228s or barcodes containing 'N' otherwise. A barcode must be 228s the last part of the read header. Values: 228s t: Remove reads with bad barcodes. 228s f: Ignore barcodes. 228s crash: Crash upon encountering bad barcodes. 228s barcodes= Comma-delimited list of barcodes or files of barcodes. 228s xmin=-1 If positive, discard reads with a lesser X coordinate. 228s ymin=-1 If positive, discard reads with a lesser Y coordinate. 228s xmax=-1 If positive, discard reads with a greater X coordinate. 228s ymax=-1 If positive, discard reads with a greater Y coordinate. 228s 228s Polymer trimming: 228s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 228s at least this length on either end of reads. 228s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 228s length on the left end of reads. Does not trim poly-C. 228s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 228s length on the right end of reads. Does not trim poly-C. 228s trimpolyg=0 This sets both left and right at once. 228s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 228s at least this length (on the left). 228s Note: there are also equivalent poly-C flags. 228s 228s Polymer tracking: 228s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 228s plen=20 Length of homopolymers to count. 228s 228s Entropy/Complexity parameters: 228s entropy=-1 Set between 0 and 1 to filter reads with entropy below 228s that value. Higher is more stringent. 228s entropywindow=50 Calculate entropy using a sliding window of this length. 228s entropyk=5 Calculate entropy using kmers of this length. 228s minbasefrequency=0 Discard reads with a minimum base frequency below this. 228s entropytrim=f Values: 228s f: (false) Do not entropy-trim. 228s r: (right) Trim low entropy on the right end only. 228s l: (left) Trim low entropy on the left end only. 228s rl: (both) Trim low entropy on both ends. 228s entropymask=f Values: 228s f: (filter) Discard low-entropy sequences. 228s t: (true) Mask low-entropy parts of sequences with N. 228s lc: Change low-entropy parts of sequences to lowercase. 228s entropymark=f Mark each base with its entropy value. This is on a scale 228s of 0-41 and is reported as quality scores, so the output 228s should be fastq or fasta+qual. 228s NOTE: If set, entropytrim overrides entropymask. 228s 228s Cardinality estimation: 228s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 228s cardinalityout=f (loglogout) Count unique kmers in output reads. 228s loglogk=31 Use this kmer length for counting. 228s loglogbuckets=2048 Use this many buckets for counting. 228s khist= Kmer frequency histogram; plots number of kmers versus 228s kmer depth. This is approximate. 228s khistout= Kmer frequency histogram for output reads. 228s 228s Java Parameters: 228s 228s -Xmx This will set Java's memory usage, overriding autodetection. 228s -Xmx20g will 228s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 228s The max is typically 85% of physical memory. 228s -eoom This flag will cause the process to exit if an 228s out-of-memory exception occurs. Requires Java 8u92+. 228s -da Disable assertions. 228s 228s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 228s 228s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 228s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 228s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 228s java -ea -Xmx1422m -Xms1422m -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 228s 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] 228s Version 39.06 228s 228s 0.038 seconds. 228s Initial: 228s Memory: max=1491m, total=1491m, free=1460m, used=31m 228s 228s Input is being processed as paired 228s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 228s Started output streams: 0.031 seconds. 228s Processing time: 0.026 seconds. 228s 228s Input: 8 reads 306 bases. 228s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 228s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 228s Result: 0 reads (0.00%) 0 bases (0.00%) 228s 228s Time: 0.079 seconds. 228s Reads Processed: 8 0.10k reads/sec 228s Bases Processed: 306 0.00m bases/sec 229s test -r out.fastq.gz 229s 229s # bbnorm 229s bbnorm.sh --version 229s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 229s java -ea -Xmx2844m -Xms2844m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 229s BBMap version 39.06 229s For help, please run the shellscript with no parameters, or look in /docs/. 229s bbnorm.sh --help 229s 229s Written by Brian Bushnell 229s Last modified October 19, 2017 229s 229s Description: Normalizes read depth based on kmer counts. 229s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 229s However, Tadpole has superior error-correction to BBNorm. 229s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 229s 229s Usage: bbnorm.sh in= out= outt= hist= 229s 229s Input parameters: 229s in=null Primary input. Use in2 for paired reads in a second file 229s in2=null Second input file for paired reads in two files 229s extra=null Additional files to use for input (generating hash table) but not for output 229s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 229s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 229s kmersample=1 Process every nth kmer, and skip the rest 229s readsample=1 Process every nth read, and skip the rest 229s 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. 229s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 229s 229s Output parameters: 229s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 229s outt= (outtoss) File for reads that were excluded from primary output 229s reads=-1 Only process this number of reads, then quit (-1 means all) 229s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 229s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 229s 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. 229s Default is false, to prevent confusion about how there can be 0-count kmers. 229s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 229s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 229s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 229s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 229s rename=f Rename reads based on their kmer depth. 229s 229s Hashing parameters: 229s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 229s 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. 229s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 229s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 229s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 229s 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. 229s prehashes=2 Number of hashes for prefilter. 229s prefilterbits=2 (pbits) Bits per cell in prefilter. 229s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 229s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 229s minq=6 Ignore kmers containing bases with quality below this 229s minprob=0.5 Ignore kmers with overall probability of correctness below this 229s 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. 229s 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. 229s 229s Normalization parameters: 229s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 229s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 229s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 229s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 229s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 229s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 229s 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. 229s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 229s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 229s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 229s 229s Error detection parameters: 229s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 229s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 229s tossbadreads=f (tbr) Throw away reads detected as containing errors. 229s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 229s 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. 229s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 229s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 229s 229s Error correction parameters: 229s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 229s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 229s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 229s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 229s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 229s eccmaxqual=127 Do not correct bases with quality above this value. 229s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 229s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 229s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 229s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 229s overlap=f (ecco) Error correct by read overlap. 229s 229s Depth binning parameters: 229s lowbindepth=10 (lbd) Cutoff for low depth bin. 229s highbindepth=80 (hbd) Cutoff for high depth bin. 229s outlow= Pairs in which both reads have a median below lbd go into this file. 229s outhigh= Pairs in which both reads have a median above hbd go into this file. 229s outmid= All other pairs go into this file. 229s 229s Histogram parameters: 229s hist= Specify a file to write the input kmer depth histogram. 229s histout= Specify a file to write the output kmer depth histogram. 229s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 229s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 229s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 229s 229s Peak calling parameters: 229s peaks= Write the peaks to this file. Default is stdout. 229s minHeight=2 (h) Ignore peaks shorter than this. 229s minVolume=5 (v) Ignore peaks with less area than this. 229s minWidth=3 (w) Ignore peaks narrower than this. 229s minPeak=2 (minp) Ignore peaks with an X-value below this. 229s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 229s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 229s 229s Java Parameters: 229s -Xmx This will set Java's memory usage, overriding autodetection. 229s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 229s The max is typically 85% of physical memory. 229s -eoom This flag will cause the process to exit if an 229s out-of-memory exception occurs. Requires Java 8u92+. 229s -da Disable assertions. 229s 229s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 229s 229s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 229s out=out3.fastq outt=outt.fastq hist=hist.plt 229s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 229s java -ea -Xmx2844m -Xms2844m -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 229s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 229s 229s 229s *********** Pass 1 ********** 229s 229s 229s Settings: 229s threads: 4 229s k: 31 229s deterministic: true 229s toss error reads: false 229s passes: 1 229s bits per cell: 16 229s cells: 1052.92M 229s hashes: 3 229s base min quality: 5 229s kmer min prob: 0.5 229s 229s target depth: 400 229s min depth: 3 229s max depth: 500 229s min good kmers: 15 229s depth percentile: 64.8 229s ignore dupe kmers: true 229s fix spikes: false 229s histogram length: 65536 229s print zero cov: false 229s 231s Made hash table: hashes = 3 mem = 1.96 GB cells = 1052.59M used = 0.000% 231s 231s Estimated unique kmers: 7 231s 231s Table creation time: 2.260 seconds. 231s Started output threads. 231s Started output threads. 231s Table read time: 0.015 seconds. 12.79 kb/sec 231s Total reads in: 2 0.000% Kept 231s Total bases in: 188 0.000% Kept 231s Error reads in: 2 100.000% 231s Error type 1: 2 100.000% 231s Error type 2: 0 0.000% 231s Error type 3: 0 0.000% 231s 231s Wrote histogram to hist.plt 232s Total kmers counted: 128 232s Total unique kmer count: 128 232s Includes forward kmers only. 232s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 232s The most accurate value is the greater of the two. 232s 232s Percent unique: 100.00% 232s Depth average: 1.00 (unique kmers) 232s Depth median: 1 (unique kmers) 232s Depth standard deviation: 0.00 (unique kmers) 232s Corrected depth average: 0.00 232s 232s Depth average: 1.00 (all kmers) 232s Depth median: 1 (all kmers) 232s Depth standard deviation: 0.00 (all kmers) 232s 232s Approx. read depth median: 1.47 232s 232s *********** Pass 2 ********** 232s 232s 232s Settings: 232s threads: 4 232s k: 31 232s deterministic: true 232s toss error reads: false 232s passes: 1 232s bits per cell: 16 232s cells: 1052.92M 232s hashes: 3 232s base min quality: 5 232s kmer min prob: 0.5 232s 232s target depth: 100 232s min depth: 5 232s max depth: 100 232s min good kmers: 15 232s depth percentile: 54.0 232s ignore dupe kmers: true 232s fix spikes: false 232s histogram length: 65536 232s 233s Made hash table: hashes = 3 mem = 1.96 GB cells = 1052.59M used = 0.000% 233s 233s Estimated unique kmers: 0 233s 233s Table creation time: 1.017 seconds. 233s Started output threads. 233s Started output threads. 233s Table read time: 0.002 seconds. 0.00 kb/sec 233s Total reads in: 0 NaN% Kept 233s Total bases in: 0 NaN% Kept 233s Error reads in: 0 NaN% 233s Error type 1: 0 NaN% 233s Error type 2: 0 NaN% 233s Error type 3: 0 NaN% 233s Total kmers counted: 0 233s Total unique kmer count: 0 233s Includes forward kmers only. 233s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 233s The most accurate value is the greater of the two. 233s 233s Percent unique: NaN% 233s Depth average: NaN (unique kmers) 233s Depth median: 0 (unique kmers) 233s Depth standard deviation: NaN (unique kmers) 233s Corrected depth average: NaN 233s 233s Depth average: NaN (all kmers) 233s Depth median: 0 (all kmers) 233s Depth standard deviation: 0.00 (all kmers) 233s 233s Approx. read depth median: NaN 233s 233s Removing temp files. 233s 233s Total time: 3.446 seconds. 0.05 kb/sec 233s test -r out3.fastq 233s test -r outt.fastq 233s test -r hist.plt 233s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 233s out=out4.fastq outt=outt2.fastq hist=hist2.plt 233s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 233s java -ea -Xmx2844m -Xms2844m -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 233s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 233s 233s 233s *********** Pass 1 ********** 233s 233s 233s Settings: 233s threads: 4 233s k: 31 233s deterministic: true 233s toss error reads: false 233s passes: 1 233s bits per cell: 16 233s cells: 1052.92M 233s hashes: 3 233s base min quality: 5 233s kmer min prob: 0.5 233s 233s target depth: 400 233s min depth: 3 233s max depth: 500 233s min good kmers: 15 233s depth percentile: 64.8 233s ignore dupe kmers: true 233s fix spikes: false 233s histogram length: 65536 233s print zero cov: false 233s 235s Made hash table: hashes = 3 mem = 1.96 GB cells = 1052.59M used = 0.000% 235s 235s Estimated unique kmers: 7 235s 235s Table creation time: 1.699 seconds. 235s Started output threads. 235s Started output threads. 235s Table read time: 0.007 seconds. 19.01 kb/sec 235s Total reads in: 2 0.000% Kept 235s Total bases in: 126 0.000% Kept 235s Error reads in: 2 100.000% 235s Error type 1: 2 100.000% 235s Error type 2: 0 0.000% 235s Error type 3: 0 0.000% 235s 235s Wrote histogram to hist2.plt 235s Total kmers counted: 66 235s Total unique kmer count: 66 235s Includes forward kmers only. 235s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 235s The most accurate value is the greater of the two. 235s 235s Percent unique: 100.00% 235s Depth average: 1.00 (unique kmers) 235s Depth median: 1 (unique kmers) 235s Depth standard deviation: 0.00 (unique kmers) 235s Corrected depth average: 0.00 235s 235s Depth average: 1.00 (all kmers) 235s Depth median: 1 (all kmers) 235s Depth standard deviation: 0.00 (all kmers) 235s 235s Approx. read depth median: 1.91 235s 235s *********** Pass 2 ********** 235s 235s 235s Settings: 235s threads: 4 235s k: 31 235s deterministic: true 235s toss error reads: false 235s passes: 1 235s bits per cell: 16 235s cells: 1052.92M 235s hashes: 3 235s base min quality: 5 235s kmer min prob: 0.5 235s 235s target depth: 100 235s min depth: 5 235s max depth: 100 235s min good kmers: 15 235s depth percentile: 54.0 235s ignore dupe kmers: true 235s fix spikes: false 235s histogram length: 65536 235s 236s Made hash table: hashes = 3 mem = 1.96 GB cells = 1052.59M used = 0.000% 236s 236s Estimated unique kmers: 0 236s 236s Table creation time: 1.002 seconds. 236s Started output threads. 236s Started output threads. 236s Table read time: 0.009 seconds. 0.00 kb/sec 236s Total reads in: 0 NaN% Kept 236s Total bases in: 0 NaN% Kept 236s Error reads in: 0 NaN% 236s Error type 1: 0 NaN% 236s Error type 2: 0 NaN% 236s Error type 3: 0 NaN% 236s Total kmers counted: 0 236s Total unique kmer count: 0 236s Includes forward kmers only. 236s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 236s The most accurate value is the greater of the two. 236s 236s Percent unique: NaN% 236s Depth average: NaN (unique kmers) 236s Depth median: 0 (unique kmers) 236s Depth standard deviation: NaN (unique kmers) 236s Corrected depth average: NaN 236s 236s Depth average: NaN (all kmers) 236s Depth median: 0 (all kmers) 236s Depth standard deviation: 0.00 (all kmers) 236s 236s Approx. read depth median: NaN 236s 236s Removing temp files. 236s 236s Total time: 2.852 seconds. 0.04 kb/sec 237s test -r out4.fastq 237s test -r outt2.fastq 237s test -r hist2.plt 237s autopkgtest [17:19:52]: test run-unit-test: -----------------------] 238s autopkgtest [17:19:53]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 238s run-unit-test PASS 238s autopkgtest [17:19:53]: @@@@@@@@@@@@@@@@@@@@ summary 238s run-unit-test PASS 250s Creating nova instance adt-noble-s390x-bbmap-20240321-171555-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240321.img (UUID f7ee8f0f-480f-4014-94f0-3be2a19e259d)...