0s autopkgtest [01:00:45]: starting date and time: 2024-03-22 01:00:45+0000 0s autopkgtest [01:00:45]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [01:00:45]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gyu4c_9p/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-3@bos02-s390x-24.secgroup --name adt-noble-s390x-bbmap-20240322-010045-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/ 96s autopkgtest [01:02:21]: testbed dpkg architecture: s390x 96s autopkgtest [01:02:21]: testbed apt version: 2.7.12 96s autopkgtest [01:02:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 97s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 97s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 97s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3765 kB] 98s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 98s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 99s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [669 kB] 99s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 99s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 99s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 99s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3987 kB] 99s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 99s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [45.1 kB] 99s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 101s Fetched 9150 kB in 3s (2709 kB/s) 101s Reading package lists... 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 104s Calculating upgrade... 105s The following packages will be upgraded: 105s cloud-init debianutils fonts-ubuntu-console python3-markupsafe 105s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Need to get 719 kB of archives. 105s After this operation, 11.3 kB disk space will be freed. 105s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x debianutils s390x 5.17 [90.1 kB] 105s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 105s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x python3-markupsafe s390x 2.1.5-1build1 [12.8 kB] 105s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x cloud-init all 24.1.2-0ubuntu1 [597 kB] 106s Preconfiguring packages ... 106s Fetched 719 kB in 1s (659 kB/s) 106s (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.) 106s Preparing to unpack .../debianutils_5.17_s390x.deb ... 106s Unpacking debianutils (5.17) over (5.16) ... 106s Setting up debianutils (5.17) ... 106s (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.) 106s Preparing to unpack .../fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 106s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 106s Preparing to unpack .../python3-markupsafe_2.1.5-1build1_s390x.deb ... 106s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 106s Preparing to unpack .../cloud-init_24.1.2-0ubuntu1_all.deb ... 107s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ... 107s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 107s Setting up cloud-init (24.1.2-0ubuntu1) ... 108s Setting up python3-markupsafe (2.1.5-1build1) ... 108s Processing triggers for man-db (2.12.0-3) ... 109s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Unknown architecture, assuming PC-style ttyS0 111s sh: Attempting to set up Debian/Ubuntu apt sources automatically 111s sh: Distribution appears to be Ubuntu 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s eatmydata is already the newest version (131-1). 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 113s dbus is already the newest version (1.14.10-4ubuntu1). 113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s rng-tools-debian is already the newest version (2.4). 113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 114s The following packages will be REMOVED: 114s cloud-init* python3-configobj* python3-debconf* 114s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 114s After this operation, 3256 kB disk space will be freed. 114s (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 ... 52170 files and directories currently installed.) 114s Removing cloud-init (24.1.2-0ubuntu1) ... 114s Removing python3-configobj (5.0.8-3) ... 114s Removing python3-debconf (1.5.86) ... 114s Processing triggers for man-db (2.12.0-3) ... 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 ... 51781 files and directories currently installed.) 115s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 115s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 115s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 115s invoke-rc.d: policy-rc.d denied execution of try-restart. 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s linux-generic is already the newest version (6.8.0-11.11+1). 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 116s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 116s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 118s Reading package lists... 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 119s Calculating upgrade... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s autopkgtest [01:02:45]: rebooting testbed after setup commands that affected boot 135s autopkgtest [01:03:00]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 138s autopkgtest [01:03:03]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 142s Get:1 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (dsc) [2286 B] 142s Get:2 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (tar) [5343 kB] 142s Get:3 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (diff) [25.4 kB] 142s gpgv: Signature made Fri Nov 24 11:00:29 2023 UTC 142s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 142s gpgv: issuer "emollier@debian.org" 142s gpgv: Can't check signature: No public key 142s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.06+dfsg-1.dsc: no acceptable signature found 143s autopkgtest [01:03:08]: testing package bbmap version 39.06+dfsg-1 143s autopkgtest [01:03:08]: build not needed 145s autopkgtest [01:03:10]: test run-unit-test: preparing testbed 152s Reading package lists... 152s Building dependency tree... 152s Reading state information... 152s Starting pkgProblemResolver with broken count: 0 152s Starting 2 pkgProblemResolver with broken count: 0 152s Done 152s The following additional packages will be installed: 152s bbmap bbmap-jni ca-certificates-java fontconfig-config fonts-dejavu-core 152s fonts-dejavu-mono java-common libapache-pom-java libasound2 libasound2-data 152s libavahi-client3 libavahi-common-data libavahi-common3 libcommons-cli-java 152s libcommons-codec-java libcommons-io-java libcommons-parent-java libcups2 152s libfontconfig1 libfreetype6 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 152s libjpeg8 liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 152s openjdk-17-jre-headless python-biopython-doc 152s Suggested packages: 152s default-jre libasound2-plugins alsa-utils libcommons-io-java-doc cups-common 152s liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd libnss-mdns 152s fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 152s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 152s Recommended packages: 152s pigz alsa-ucm-conf alsa-topology-conf python3-biopython 152s The following NEW packages will be installed: 152s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java fontconfig-config 152s fonts-dejavu-core fonts-dejavu-mono java-common libapache-pom-java 152s libasound2 libasound2-data libavahi-client3 libavahi-common-data 152s libavahi-common3 libcommons-cli-java libcommons-codec-java 152s libcommons-io-java libcommons-parent-java libcups2 libfontconfig1 152s libfreetype6 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 liblcms2-2 152s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 152s python-biopython-doc 152s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 152s Need to get 78.1 MB/78.1 MB of archives. 152s After this operation, 226 MB of additional disk space will be used. 152s Get:1 /tmp/autopkgtest.B82BfY/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [724 B] 152s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-cli-java all 1.6.0-1 [59.9 kB] 153s Get:3 http://ftpmaster.internal/ubuntu noble/universe s390x libapache-pom-java all 29-2 [5284 B] 153s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-parent-java all 56-1 [10.7 kB] 153s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-codec-java all 1.16.0-1 [306 kB] 153s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-io-java all 2.11.0-2 [297 kB] 153s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x liblog4j1.2-java all 1.2.17-11 [439 kB] 153s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x libmpj-java all 0.44+dfsg-4 [443 kB] 153s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x ca-certificates-java all 20240118 [11.6 kB] 153s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x java-common all 0.75+exp1 [6798 B] 153s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libavahi-common-data s390x 0.8-13ubuntu2 [29.5 kB] 153s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libavahi-common3 s390x 0.8-13ubuntu2 [23.8 kB] 153s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libavahi-client3 s390x 0.8-13ubuntu2 [26.7 kB] 153s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libcups2 s390x 2.4.6-0ubuntu3 [277 kB] 153s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x liblcms2-2 s390x 2.14-2 [155 kB] 153s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB] 153s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 153s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libfreetype6 s390x 2.13.2+dfsg-1 [431 kB] 154s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 154s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 154s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig-config s390x 2.15.0-1ubuntu1 [37.0 kB] 154s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libfontconfig1 s390x 2.15.0-1ubuntu1 [150 kB] 154s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libasound2-data all 1.2.10-3build1 [20.7 kB] 154s Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libasound2 s390x 1.2.10-3build1 [414 kB] 154s Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2 [90.4 kB] 154s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libharfbuzz0b s390x 8.3.0-2 [515 kB] 154s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libpcsclite1 s390x 2.0.0-1 [19.9 kB] 154s Get:28 http://ftpmaster.internal/ubuntu noble/main s390x openjdk-17-jre-headless s390x 17.0.10+7-1 [45.7 MB] 157s Get:29 http://ftpmaster.internal/ubuntu noble/universe s390x bbmap all 39.06+dfsg-1 [9768 kB] 157s Get:30 http://ftpmaster.internal/ubuntu noble/universe s390x bbmap-jni s390x 39.06+dfsg-1 [38.7 kB] 157s Get:31 http://ftpmaster.internal/ubuntu noble/universe s390x python-biopython-doc all 1.81+dfsg-3 [17.3 MB] 158s Fetched 78.1 MB in 5s (15.1 MB/s) 158s Selecting previously unselected package libcommons-cli-java. 158s (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 ... 51726 files and directories currently installed.) 158s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 158s Unpacking libcommons-cli-java (1.6.0-1) ... 158s Selecting previously unselected package libapache-pom-java. 158s Preparing to unpack .../01-libapache-pom-java_29-2_all.deb ... 158s Unpacking libapache-pom-java (29-2) ... 158s Selecting previously unselected package libcommons-parent-java. 158s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 158s Unpacking libcommons-parent-java (56-1) ... 158s Selecting previously unselected package libcommons-codec-java. 158s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 158s Unpacking libcommons-codec-java (1.16.0-1) ... 158s Selecting previously unselected package libcommons-io-java. 158s Preparing to unpack .../04-libcommons-io-java_2.11.0-2_all.deb ... 158s Unpacking libcommons-io-java (2.11.0-2) ... 158s Selecting previously unselected package liblog4j1.2-java. 158s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 158s Unpacking liblog4j1.2-java (1.2.17-11) ... 158s Selecting previously unselected package libmpj-java. 158s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 158s Unpacking libmpj-java (0.44+dfsg-4) ... 158s Selecting previously unselected package ca-certificates-java. 158s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 158s Unpacking ca-certificates-java (20240118) ... 158s Selecting previously unselected package java-common. 158s Preparing to unpack .../08-java-common_0.75+exp1_all.deb ... 158s Unpacking java-common (0.75+exp1) ... 158s Selecting previously unselected package libavahi-common-data:s390x. 158s Preparing to unpack .../09-libavahi-common-data_0.8-13ubuntu2_s390x.deb ... 158s Unpacking libavahi-common-data:s390x (0.8-13ubuntu2) ... 158s Selecting previously unselected package libavahi-common3:s390x. 158s Preparing to unpack .../10-libavahi-common3_0.8-13ubuntu2_s390x.deb ... 158s Unpacking libavahi-common3:s390x (0.8-13ubuntu2) ... 158s Selecting previously unselected package libavahi-client3:s390x. 158s Preparing to unpack .../11-libavahi-client3_0.8-13ubuntu2_s390x.deb ... 158s Unpacking libavahi-client3:s390x (0.8-13ubuntu2) ... 158s Selecting previously unselected package libcups2:s390x. 158s Preparing to unpack .../12-libcups2_2.4.6-0ubuntu3_s390x.deb ... 158s Unpacking libcups2:s390x (2.4.6-0ubuntu3) ... 158s Selecting previously unselected package liblcms2-2:s390x. 158s Preparing to unpack .../13-liblcms2-2_2.14-2_s390x.deb ... 158s Unpacking liblcms2-2:s390x (2.14-2) ... 158s Selecting previously unselected package libjpeg-turbo8:s390x. 158s Preparing to unpack .../14-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ... 158s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 158s Selecting previously unselected package libjpeg8:s390x. 158s Preparing to unpack .../15-libjpeg8_8c-2ubuntu11_s390x.deb ... 158s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 158s Selecting previously unselected package libfreetype6:s390x. 158s Preparing to unpack .../16-libfreetype6_2.13.2+dfsg-1_s390x.deb ... 158s Unpacking libfreetype6:s390x (2.13.2+dfsg-1) ... 158s Selecting previously unselected package fonts-dejavu-mono. 158s Preparing to unpack .../17-fonts-dejavu-mono_2.37-8_all.deb ... 158s Unpacking fonts-dejavu-mono (2.37-8) ... 158s Selecting previously unselected package fonts-dejavu-core. 158s Preparing to unpack .../18-fonts-dejavu-core_2.37-8_all.deb ... 158s Unpacking fonts-dejavu-core (2.37-8) ... 158s Selecting previously unselected package fontconfig-config. 158s Preparing to unpack .../19-fontconfig-config_2.15.0-1ubuntu1_s390x.deb ... 159s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 159s Selecting previously unselected package libfontconfig1:s390x. 159s Preparing to unpack .../20-libfontconfig1_2.15.0-1ubuntu1_s390x.deb ... 159s Unpacking libfontconfig1:s390x (2.15.0-1ubuntu1) ... 159s Selecting previously unselected package libasound2-data. 159s Preparing to unpack .../21-libasound2-data_1.2.10-3build1_all.deb ... 159s Unpacking libasound2-data (1.2.10-3build1) ... 159s Selecting previously unselected package libasound2:s390x. 159s Preparing to unpack .../22-libasound2_1.2.10-3build1_s390x.deb ... 159s Unpacking libasound2:s390x (1.2.10-3build1) ... 159s Selecting previously unselected package libgraphite2-3:s390x. 159s Preparing to unpack .../23-libgraphite2-3_1.3.14-2_s390x.deb ... 159s Unpacking libgraphite2-3:s390x (1.3.14-2) ... 159s Selecting previously unselected package libharfbuzz0b:s390x. 159s Preparing to unpack .../24-libharfbuzz0b_8.3.0-2_s390x.deb ... 159s Unpacking libharfbuzz0b:s390x (8.3.0-2) ... 159s Selecting previously unselected package libpcsclite1:s390x. 159s Preparing to unpack .../25-libpcsclite1_2.0.0-1_s390x.deb ... 159s Unpacking libpcsclite1:s390x (2.0.0-1) ... 159s Selecting previously unselected package openjdk-17-jre-headless:s390x. 159s Preparing to unpack .../26-openjdk-17-jre-headless_17.0.10+7-1_s390x.deb ... 159s Unpacking openjdk-17-jre-headless:s390x (17.0.10+7-1) ... 160s Selecting previously unselected package bbmap. 160s Preparing to unpack .../27-bbmap_39.06+dfsg-1_all.deb ... 160s Unpacking bbmap (39.06+dfsg-1) ... 160s Selecting previously unselected package bbmap-jni. 160s Preparing to unpack .../28-bbmap-jni_39.06+dfsg-1_s390x.deb ... 160s Unpacking bbmap-jni (39.06+dfsg-1) ... 160s Selecting previously unselected package python-biopython-doc. 160s Preparing to unpack .../29-python-biopython-doc_1.81+dfsg-3_all.deb ... 160s Unpacking python-biopython-doc (1.81+dfsg-3) ... 161s Selecting previously unselected package autopkgtest-satdep. 161s Preparing to unpack .../30-1-autopkgtest-satdep.deb ... 161s Unpacking autopkgtest-satdep (0) ... 161s Setting up libgraphite2-3:s390x (1.3.14-2) ... 161s Setting up liblcms2-2:s390x (2.14-2) ... 161s Setting up java-common (0.75+exp1) ... 161s Setting up libcommons-cli-java (1.6.0-1) ... 161s Setting up liblog4j1.2-java (1.2.17-11) ... 161s Setting up libasound2-data (1.2.10-3build1) ... 161s Setting up libfreetype6:s390x (2.13.2+dfsg-1) ... 161s Setting up libapache-pom-java (29-2) ... 161s Setting up libavahi-common-data:s390x (0.8-13ubuntu2) ... 161s Setting up fonts-dejavu-mono (2.37-8) ... 161s Setting up fonts-dejavu-core (2.37-8) ... 161s Setting up libpcsclite1:s390x (2.0.0-1) ... 161s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 161s Setting up python-biopython-doc (1.81+dfsg-3) ... 161s Setting up libasound2:s390x (1.2.10-3build1) ... 161s Setting up libharfbuzz0b:s390x (8.3.0-2) ... 161s Setting up bbmap-jni (39.06+dfsg-1) ... 161s Setting up ca-certificates-java (20240118) ... 161s No JRE found. Skipping Java certificates setup. 161s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 161s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 161s Setting up libcommons-parent-java (56-1) ... 161s Setting up libavahi-common3:s390x (0.8-13ubuntu2) ... 161s Setting up libfontconfig1:s390x (2.15.0-1ubuntu1) ... 161s Setting up libcommons-codec-java (1.16.0-1) ... 161s Setting up libavahi-client3:s390x (0.8-13ubuntu2) ... 161s Setting up libcommons-io-java (2.11.0-2) ... 161s Setting up libmpj-java (0.44+dfsg-4) ... 161s Setting up libcups2:s390x (2.4.6-0ubuntu3) ... 161s Setting up openjdk-17-jre-headless:s390x (17.0.10+7-1) ... 161s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/java to provide /usr/bin/java (java) in auto mode 161s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 161s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 161s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 161s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 161s Processing triggers for libc-bin (2.39-0ubuntu2) ... 161s Processing triggers for man-db (2.12.0-3) ... 162s Processing triggers for ca-certificates-java (20240118) ... 162s Adding debian:ACCVRAIZ1.pem 162s Adding debian:AC_RAIZ_FNMT-RCM.pem 162s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 162s Adding debian:ANF_Secure_Server_Root_CA.pem 162s Adding debian:Actalis_Authentication_Root_CA.pem 162s Adding debian:AffirmTrust_Commercial.pem 162s Adding debian:AffirmTrust_Networking.pem 162s Adding debian:AffirmTrust_Premium.pem 162s Adding debian:AffirmTrust_Premium_ECC.pem 162s Adding debian:Amazon_Root_CA_1.pem 162s Adding debian:Amazon_Root_CA_2.pem 162s Adding debian:Amazon_Root_CA_3.pem 162s Adding debian:Amazon_Root_CA_4.pem 162s Adding debian:Atos_TrustedRoot_2011.pem 162s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 162s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 162s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 162s Adding debian:BJCA_Global_Root_CA1.pem 162s Adding debian:BJCA_Global_Root_CA2.pem 162s Adding debian:Baltimore_CyberTrust_Root.pem 162s Adding debian:Buypass_Class_2_Root_CA.pem 162s Adding debian:Buypass_Class_3_Root_CA.pem 162s Adding debian:CA_Disig_Root_R2.pem 162s Adding debian:CFCA_EV_ROOT.pem 162s Adding debian:COMODO_Certification_Authority.pem 162s Adding debian:COMODO_ECC_Certification_Authority.pem 162s Adding debian:COMODO_RSA_Certification_Authority.pem 162s Adding debian:Certainly_Root_E1.pem 162s Adding debian:Certainly_Root_R1.pem 162s Adding debian:Certigna.pem 162s Adding debian:Certigna_Root_CA.pem 162s Adding debian:Certum_EC-384_CA.pem 162s Adding debian:Certum_Trusted_Network_CA.pem 162s Adding debian:Certum_Trusted_Network_CA_2.pem 162s Adding debian:Certum_Trusted_Root_CA.pem 162s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 162s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 162s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 162s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 162s Adding debian:Comodo_AAA_Services_root.pem 162s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 162s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 162s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 162s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 162s Adding debian:DigiCert_Assured_ID_Root_CA.pem 162s Adding debian:DigiCert_Assured_ID_Root_G2.pem 162s Adding debian:DigiCert_Assured_ID_Root_G3.pem 162s Adding debian:DigiCert_Global_Root_CA.pem 162s Adding debian:DigiCert_Global_Root_G2.pem 162s Adding debian:DigiCert_Global_Root_G3.pem 162s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 162s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 162s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 162s Adding debian:DigiCert_Trusted_Root_G4.pem 162s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 162s Adding debian:Entrust_Root_Certification_Authority.pem 162s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 162s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 162s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 162s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 162s Adding debian:GLOBALTRUST_2020.pem 162s Adding debian:GTS_Root_R1.pem 162s Adding debian:GTS_Root_R2.pem 162s Adding debian:GTS_Root_R3.pem 162s Adding debian:GTS_Root_R4.pem 162s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 162s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 162s Adding debian:GlobalSign_Root_CA.pem 162s Adding debian:GlobalSign_Root_CA_-_R3.pem 162s Adding debian:GlobalSign_Root_CA_-_R6.pem 162s Adding debian:GlobalSign_Root_E46.pem 162s Adding debian:GlobalSign_Root_R46.pem 162s Adding debian:Go_Daddy_Class_2_CA.pem 162s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 162s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 162s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 162s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 162s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 162s Adding debian:HiPKI_Root_CA_-_G1.pem 162s Adding debian:Hongkong_Post_Root_CA_3.pem 162s Adding debian:ISRG_Root_X1.pem 162s Adding debian:ISRG_Root_X2.pem 162s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 162s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 162s Adding debian:Izenpe.com.pem 162s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 162s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 162s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 162s Adding debian:NAVER_Global_Root_Certification_Authority.pem 162s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 162s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 162s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 162s Adding debian:QuoVadis_Root_CA_1_G3.pem 162s Adding debian:QuoVadis_Root_CA_2.pem 162s Adding debian:QuoVadis_Root_CA_2_G3.pem 162s Adding debian:QuoVadis_Root_CA_3.pem 162s Adding debian:QuoVadis_Root_CA_3_G3.pem 162s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 162s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 162s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 162s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 162s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 162s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 162s Adding debian:SZAFIR_ROOT_CA2.pem 162s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 162s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 162s Adding debian:SecureSign_RootCA11.pem 162s Adding debian:SecureTrust_CA.pem 162s Adding debian:Secure_Global_CA.pem 162s Adding debian:Security_Communication_ECC_RootCA1.pem 162s Adding debian:Security_Communication_RootCA2.pem 162s Adding debian:Security_Communication_RootCA3.pem 162s Adding debian:Security_Communication_Root_CA.pem 162s Adding debian:Starfield_Class_2_CA.pem 162s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 162s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 162s Adding debian:SwissSign_Gold_CA_-_G2.pem 162s Adding debian:SwissSign_Silver_CA_-_G2.pem 162s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 162s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 162s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 162s Adding debian:TWCA_Global_Root_CA.pem 162s Adding debian:TWCA_Root_Certification_Authority.pem 162s Adding debian:TeliaSonera_Root_CA_v1.pem 162s Adding debian:Telia_Root_CA_v2.pem 162s Adding debian:TrustAsia_Global_Root_CA_G3.pem 162s Adding debian:TrustAsia_Global_Root_CA_G4.pem 162s Adding debian:Trustwave_Global_Certification_Authority.pem 162s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 162s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 162s Adding debian:TunTrust_Root_CA.pem 162s Adding debian:UCA_Extended_Validation_Root.pem 162s Adding debian:UCA_Global_G2_Root.pem 162s Adding debian:USERTrust_ECC_Certification_Authority.pem 162s Adding debian:USERTrust_RSA_Certification_Authority.pem 162s Adding debian:XRamp_Global_CA_Root.pem 162s Adding debian:certSIGN_ROOT_CA.pem 162s Adding debian:certSIGN_Root_CA_G2.pem 162s Adding debian:e-Szigno_Root_CA_2017.pem 162s Adding debian:ePKI_Root_Certification_Authority.pem 162s Adding debian:emSign_ECC_Root_CA_-_C3.pem 162s Adding debian:emSign_ECC_Root_CA_-_G3.pem 162s Adding debian:emSign_Root_CA_-_C1.pem 162s Adding debian:emSign_Root_CA_-_G1.pem 162s Adding debian:vTrus_ECC_Root_CA.pem 162s Adding debian:vTrus_Root_CA.pem 162s done. 162s Setting up bbmap (39.06+dfsg-1) ... 162s Setting up autopkgtest-satdep (0) ... 165s (Reading database ... 54568 files and directories currently installed.) 165s Removing autopkgtest-satdep (0) ... 166s autopkgtest [01:03:31]: test run-unit-test: [----------------------- 166s 166s # bbmap 166s bbmap.sh --version 166s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 166s java -ea -Xmx2844m -Xms2844m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 167s BBMap version 39.06 167s For help, please run the shellscript with no parameters, or look in /docs/. 167s bbmap.sh --help 167s bbmap.sh ref=example.fasta 167s 167s BBMap 167s Written by Brian Bushnell, from Dec. 2010 - present 167s Last modified September 15, 2022 167s 167s Description: Fast and accurate splice-aware read aligner. 167s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 167s 167s To index: bbmap.sh ref= 167s To map: bbmap.sh in= out= 167s To map without writing an index: 167s bbmap.sh ref= in= out= nodisk 167s 167s in=stdin will accept reads from standard in, and out=stdout will write to 167s standard out, but file extensions are still needed to specify the format of the 167s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 167s standard in; out=stdout.sam.gz will write gzipped sam. 167s 167s Indexing Parameters (required when building the index): 167s nodisk=f Set to true to build index in memory and write nothing 167s to disk except output. 167s ref= Specify the reference sequence. Only do this ONCE, 167s when building the index (unless using 'nodisk'). 167s build=1 If multiple references are indexed in the same directory, 167s each needs a unique numeric ID (unless using 'nodisk'). 167s k=13 Kmer length, range 8-15. Longer is faster but uses 167s more memory. Shorter is more sensitive. 167s If indexing and mapping are done in two steps, K should 167s be specified each time. 167s path=<.> Specify the location to write the index, if you don't 167s want it in the current working directory. 167s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 167s number (reduces RAM by 50% and sensitivity slightly). 167s Should be enabled both when building the index AND 167s when mapping. 167s rebuild=f Force a rebuild of the index (ref= should be set). 167s 167s Input Parameters: 167s build=1 Designate index to use. Corresponds to the number 167s specified when building the index. 167s in= Primary reads input; required parameter. 167s in2= For paired reads in two files. 167s interleaved=auto True forces paired/interleaved input; false forces 167s single-ended mapping. If not specified, interleaved 167s status will be autodetected from read names. 167s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 167s BBMap and 6000 for BBMapPacBio. Only works for FASTA 167s input (use 'maxlen' for FASTQ input). The default for 167s bbmap.sh is 500, and for mapPacBio.sh is 6000. 167s unpigz=f Spawn a pigz (parallel gzip) process for faster 167s decompression than using Java. 167s Requires pigz to be installed. 167s touppercase=t (tuc) Convert lowercase letters in reads to upper case 167s (otherwise they will not match the reference). 167s 167s Sampling Parameters: 167s 167s reads=-1 Set to a positive number N to only process the first N 167s reads (or pairs), then quit. -1 means use all reads. 167s samplerate=1 Set to a number from 0 to 1 to randomly select that 167s fraction of reads for mapping. 1 uses all reads. 167s skipreads=0 Set to a number N to skip the first N reads (or pairs), 167s then map the rest. 167s 167s Mapping Parameters: 167s fast=f This flag is a macro which sets other paramters to run 167s faster, at reduced sensitivity. Bad for RNA-seq. 167s slow=f This flag is a macro which sets other paramters to run 167s slower, at greater sensitivity. 'vslow' is even slower. 167s maxindel=16000 Don't look for indels longer than this. Lower is faster. 167s Set to >=100k for RNAseq with long introns like mammals. 167s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 167s By default these are not sought, but may be found anyway. 167s tipsearch=100 Look this far for read-end deletions with anchors 167s shorter than K, using brute force. 167s minid=0.76 Approximate minimum alignment identity to look for. 167s Higher is faster and less sensitive. 167s minhits=1 Minimum number of seed hits required for candidate sites. 167s Higher is faster. 167s local=f Set to true to use local, rather than global, alignments. 167s This will soft-clip ugly ends of poor alignments. 167s perfectmode=f Allow only perfect mappings when set to true (very fast). 167s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 167s N's in the reference) mappings. 167s threads=auto (t) Set to number of threads desired. By default, uses 167s all cores available. 167s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 167s multiple top-scoring mapping locations). 167s best (use the first best site) 167s toss (consider unmapped) 167s random (select one top-scoring site randomly) 167s all (retain all top-scoring sites) 167s samestrandpairs=f (ssp) Specify whether paired reads should map to the 167s same strand or opposite strands. 167s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 167s orientation. Set to false for long-mate-pair libraries. 167s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 167s insert size or orientation, the read with the lower 167s mapping quality is marked unmapped. 167s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 167s be sent to 'outu' but not 'outm'. 167s rcomp=f Reverse complement both reads prior to mapping (for LMP 167s outward-facing libraries). 167s rcompmate=f Reverse complement read2 prior to mapping. 167s pairlen=32000 Set max allowed distance between paired reads. 167s (insert size)=(pairlen)+(read1 length)+(read2 length) 167s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 167s greater than this. Lower is faster. 167s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 167s is faster. 167s averagepairdist=100 (apd) Initial average distance between paired reads. 167s Varies dynamically; does not need to be specified. 167s deterministic=f Run in deterministic mode. In this case it is good 167s to set averagepairdist. BBMap is deterministic 167s without this flag if using single-ended reads, 167s or run singlethreaded. 167s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 167s fraction of read length. Faster but less accurate. 167s bandwidth=0 (bw) Set the bandwidth directly. 167s fraction of read length. Faster but less accurate. 167s usejni=f (jni) Do alignments faster, in C code. Requires 167s compiling the C code; details are in /jni/README.txt. 167s maxsites2=800 Don't analyze (or print) more than this many alignments 167s per read. 167s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 167s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 167s will ignore the most common 3% of kmers. 167s greedy=t Use a greedy algorithm to discard the least-useful 167s kmers on a per-read basis. 167s kfilter=0 If positive, potential mapping sites must have at 167s least this many consecutive exact matches. 167s 167s 167s Quality and Trimming Parameters: 167s qin=auto Set to 33 or 64 to specify input quality value ASCII 167s offset. 33 is Sanger, 64 is old Solexa. 167s qout=auto Set to 33 or 64 to specify output quality value ASCII 167s offset (only if output format is fastq). 167s qtrim=f Quality-trim ends before mapping. Options are: 167s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 167s untrim=f Undo trimming after mapping. Untrimmed bases will be 167s soft-clipped in cigar strings. 167s trimq=6 Trim regions with average quality below this 167s (phred algorithm). 167s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 167s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 167s quality strings for fasta input reads. 167s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 167s out-of-range quality values. 167s usequality=t Use quality scores when determining which read kmers 167s to use as seeds. 167s minaveragequality=0 (maq) Do not map reads with average quality below this. 167s maqb=0 If positive, calculate maq from this many initial bases. 167s 167s Output Parameters: 167s out= Write all reads to this file. 167s outu= Write only unmapped reads to this file. Does not 167s include unmapped paired reads with a mapped mate. 167s outm= Write only mapped reads to this file. Includes 167s unmapped paired reads with a mapped mate. 167s mappedonly=f If true, treats 'out' like 'outm'. 167s bamscript= (bs) Write a shell script to that will turn 167s the sam output into a sorted, indexed bam file. 167s ordered=f Set to true to output reads in same order as input. 167s Slower and uses more memory. 167s overwrite=f (ow) Allow process to overwrite existing files. 167s secondary=f Print secondary alignments. 167s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 167s with score of at least this fraction of primary. 167s ssao=f (secondarysiteasambiguousonly) Only print secondary 167s alignments for ambiguously-mapped reads. 167s maxsites=5 Maximum number of total alignments to print per read. 167s Only relevant when secondary=t. 167s quickmatch=f Generate cigar strings more quickly. 167s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 167s assuming that the remainder is a comment or description. 167s ziplevel=2 (zl) Compression level for zip or gzip output. 167s pigz=f Spawn a pigz (parallel gzip) process for faster 167s compression than Java. Requires pigz to be installed. 167s machineout=f Set to true to output statistics in machine-friendly 167s 'key=value' format. 167s printunmappedcount=f Print the total number of unmapped reads and bases. 167s If input is paired, the number will be of pairs 167s for which both reads are unmapped. 167s showprogress=0 If positive, print a '.' every X reads. 167s showprogress2=0 If positive, print the number of seconds since the 167s last progress update (instead of a '.'). 167s renamebyinsert=f Renames reads based on their mapped insert size. 167s 167s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 167s bloom=f Use a Bloom filter to ignore reads not sharing kmers 167s with the reference. This uses more memory, but speeds 167s mapping when most reads don't match the reference. 167s bloomhashes=2 Number of hash functions. 167s bloomminhits=3 Number of consecutive hits to be considered matched. 167s bloomk=31 Bloom filter kmer length. 167s bloomserial=t Use the serialized Bloom filter for greater loading 167s speed, if available. If not, generate and write one. 167s 167s Post-Filtering Parameters: 167s idfilter=0 Independant of minid; sets exact minimum identity 167s allowed for alignments to be printed. Range 0 to 1. 167s subfilter=-1 Ban alignments with more than this many substitutions. 167s insfilter=-1 Ban alignments with more than this many insertions. 167s delfilter=-1 Ban alignments with more than this many deletions. 167s indelfilter=-1 Ban alignments with more than this many indels. 167s editfilter=-1 Ban alignments with more than this many edits. 167s inslenfilter=-1 Ban alignments with an insertion longer than this. 167s dellenfilter=-1 Ban alignments with a deletion longer than this. 167s nfilter=-1 Ban alignments with more than this many ns. This 167s includes nocall, noref, and off scaffold ends. 167s 167s Sam flags and settings: 167s noheader=f Disable generation of header lines. 167s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 167s with = and X, or 1.3 to use M. 167s saa=t (secondaryalignmentasterisks) Use asterisks instead of 167s bases for sam secondary alignments. 167s cigar=t Set to 'f' to skip generation of cigar strings (faster). 167s keepnames=f Keep original names of paired reads, rather than 167s ensuring both reads have the same name. 167s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 167s cigar strings for deletions of at least that length. 167s rgid= Set readgroup ID. All other readgroup fields 167s can be set similarly, with the flag rgXX= 167s If you set a readgroup flag to the word 'filename', 167s e.g. rgid=filename, the input file name will be used. 167s mdtag=f Write MD tags. 167s nhtag=f Write NH tags. 167s xmtag=f Write XM tags (may only work correctly with ambig=all). 167s amtag=f Write AM tags. 167s nmtag=f Write NM tags. 167s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 167s for RNAseq using firststrand, secondstrand, or 167s unstranded libraries. Needed by Cufflinks. 167s JGI mainly uses 'firststrand'. 167s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 167s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 167s prefixed by YL:Z: 167s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 167s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 167s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 167s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 167s boundstag=f Write a tag indicating whether either read in the pair 167s goes off the end of the reference, prefixed by XB:Z: 167s notags=f Turn off all optional tags. 167s 167s Histogram and statistics output parameters: 167s scafstats= Statistics on how many reads mapped to which scaffold. 167s refstats= Statistics on how many reads mapped to which reference 167s file; only for BBSplit. 167s sortscafs=t Sort scaffolds or references by read count. 167s bhist= Base composition histogram by position. 167s qhist= Quality histogram by position. 167s aqhist= Histogram of average read quality. 167s bqhist= Quality histogram designed for box plots. 167s lhist= Read length histogram. 167s ihist= Write histogram of insert sizes (for paired reads). 167s ehist= Errors-per-read histogram. 167s qahist= Quality accuracy histogram of error rates versus 167s quality score. 167s indelhist= Indel length histogram. 167s mhist= Histogram of match, sub, del, and ins rates by 167s read location. 167s gchist= Read GC content histogram. 167s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 167s gcpairs=t Use average GC of paired reads. 167s idhist= Histogram of read count versus percent identity. 167s idbins=100 Number idhist bins. Set to 'auto' to use read length. 167s statsfile=stderr Mapping statistics are printed here. 167s 167s Coverage output parameters (these may reduce speed and use more RAM): 167s covstats= Per-scaffold coverage info. 167s rpkm= Per-scaffold RPKM/FPKM counts. 167s covhist= Histogram of # occurrences of each depth level. 167s basecov= Coverage per base location. 167s bincov= Print binned coverage per location (one line per X bases). 167s covbinsize=1000 Set the binsize for binned coverage output. 167s nzo=t Only print scaffolds with nonzero coverage. 167s twocolumn=f Change to true to print only ID and Avg_fold instead of 167s all 6 columns to the 'out=' file. 167s 32bit=f Set to true if you need per-base coverage over 64k. 167s strandedcov=f Track coverage for plus and minus strand independently. 167s startcov=f Only track start positions of reads. 167s secondarycov=t Include coverage of secondary alignments. 167s physcov=f Calculate physical coverage for paired reads. 167s This includes the unsequenced bases. 167s delcoverage=t (delcov) Count bases covered by deletions as covered. 167s True is faster than false. 167s covk=0 If positive, calculate kmer coverage statistics. 167s 167s Java Parameters: 167s -Xmx This will set Java's memory usage, 167s overriding autodetection. 167s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 167s will specify 800 megs. The max is typically 85% of 167s physical memory. The human genome requires around 24g, 167s or 12g with the 'usemodulo' flag. The index uses 167s roughly 6 bytes per reference base. 167s -eoom This flag will cause the process to exit if an 167s out-of-memory exception occurs. Requires Java 8u92+. 167s -da Disable assertions. 167s 167s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 167s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 167s 167s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 167s java -ea -Xmx2845m -Xms2845m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 167s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 167s Version 39.06 167s 167s No output file. 167s Writing reference. 167s 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] 167s 167s Set genScaffoldInfo=true 167s Writing chunk 1 167s Set genome to 1 167s 167s Loaded Reference: 0.004 seconds. 167s Loading index for chunk 1-1, build 1 167s No index available; generating from reference genome: /tmp/autopkgtest.B82BfY/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 167s Indexing threads started for block 0-1 167s Indexing threads finished for block 0-1 168s Generated Index: 1.539 seconds. 168s No reads to process; quitting. 168s 168s Total time: 1.650 seconds. 168s test -d ref 168s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 168s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 168s 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 169s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 169s Version 39.06 169s 169s Retaining first best site only for ambiguous mappings. 169s Set genome to 1 169s 169s Loaded Reference: 0.017 seconds. 169s Loading index for chunk 1-1, build 1 169s Generated Index: 0.781 seconds. 175s Analyzed Index: 5.934 seconds. 175s Started output stream: 0.016 seconds. 175s Cleared Memory: 0.126 seconds. 176s Processing reads in single-ended mode. 176s Started read stream. 176s Started 4 mapping threads. 176s Detecting finished threads: 0, 1, 2, 3 176s 176s ------------------ Results ------------------ 176s 176s Genome: 1 176s Key Length: 13 176s Max Indel: 16000 176s Minimum Score Ratio: 0.56 176s Mapping Mode: normal 176s Reads Used: 4 (153 bases) 176s 176s Mapping: 0.149 seconds. 176s Reads/sec: 26.92 176s kBases/sec: 1.03 176s 176s 176s Read 1 data: pct reads num reads pct bases num bases 176s 176s mapped: 0.0000% 0 0.0000% 0 176s unambiguous: 0.0000% 0 0.0000% 0 176s ambiguous: 0.0000% 0 0.0000% 0 176s low-Q discards: 25.0000% 1 19.6078% 30 176s 176s perfect best site: 0.0000% 0 0.0000% 0 176s semiperfect site: 0.0000% 0 0.0000% 0 176s 176s Match Rate: NA NA NaN% 0 176s Error Rate: NaN% 0 NaN% 0 176s Sub Rate: NaN% 0 NaN% 0 176s Del Rate: NaN% 0 NaN% 0 176s Ins Rate: NaN% 0 NaN% 0 176s N Rate: NaN% 0 NaN% 0 176s 176s Total time: 7.121 seconds. 176s test -r out.sam 176s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 176s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 176s java -ea -Xmx2845m -Xms2845m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 176s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 176s Version 39.06 176s 176s Retaining first best site only for ambiguous mappings. 176s 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] 176s 176s Set genScaffoldInfo=true 176s Set genome to 1 176s 176s Loaded Reference: 0.001 seconds. 176s Loading index for chunk 1-1, build 1 176s Indexing threads started for block 0-1 176s Indexing threads finished for block 0-1 176s Generated Index: 0.385 seconds. 182s Analyzed Index: 5.715 seconds. 182s Started output stream: 0.019 seconds. 182s Cleared Memory: 0.123 seconds. 182s Processing reads in single-ended mode. 182s Started read stream. 182s Started 4 mapping threads. 182s Detecting finished threads: 0, 1, 2, 3 182s 182s ------------------ Results ------------------ 182s 182s Genome: 1 182s Key Length: 13 182s Max Indel: 16000 182s Minimum Score Ratio: 0.56 182s Mapping Mode: normal 182s Reads Used: 3 (75 bases) 182s 182s Mapping: 0.099 seconds. 182s Reads/sec: 30.33 182s kBases/sec: 0.76 182s 182s 182s Read 1 data: pct reads num reads pct bases num bases 182s 182s mapped: 100.0000% 3 100.0000% 75 182s unambiguous: 100.0000% 3 100.0000% 75 182s ambiguous: 0.0000% 0 0.0000% 0 182s low-Q discards: 0.0000% 0 0.0000% 0 182s 182s perfect best site: 100.0000% 3 100.0000% 75 182s semiperfect site: 100.0000% 3 100.0000% 75 182s 182s Match Rate: NA NA 100.0000% 75 182s Error Rate: 0.0000% 0 0.0000% 0 182s Sub Rate: 0.0000% 0 0.0000% 0 182s Del Rate: 0.0000% 0 0.0000% 0 182s Ins Rate: 0.0000% 0 0.0000% 0 182s N Rate: 0.0000% 0 0.0000% 0 182s 182s Total time: 6.442 seconds. 182s test -r out2.sam 182s 182s # bbduk 182s bbduk.sh --version 182s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 182s java -ea -Xmx1422m -Xms1422m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 183s BBMap version 39.06 183s For help, please run the shellscript with no parameters, or look in /docs/. 183s bbduk.sh --help 183s 183s Written by Brian Bushnell 183s Last modified November 9, 2023 183s 183s Description: Compares reads to the kmers in a reference dataset, optionally 183s allowing an edit distance. Splits the reads into two outputs - those that 183s match the reference, and those that don't. Can also trim (remove) the matching 183s parts of the reads rather than binning the reads. 183s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 183s 183s Usage: bbduk.sh in= out= ref= 183s 183s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 183s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 183s fasta input, set in=stdin.fa.gz 183s 183s Input parameters: 183s in= Main input. in=stdin.fq will pipe from stdin. 183s in2= Input for 2nd read of pairs in a different file. 183s ref= Comma-delimited list of reference files. 183s In addition to filenames, you may also use the keywords: 183s adapters, artifacts, phix, lambda, pjet, mtst, kapa 183s literal= Comma-delimited list of literal reference sequences. 183s touppercase=f (tuc) Change all bases upper-case. 183s interleaved=auto (int) t/f overrides interleaved autodetection. 183s Must be set mainually when streaming fastq input. 183s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 183s reads=-1 If positive, quit after processing X reads or pairs. 183s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 183s possible unambiguous copies. Intended for short motifs 183s or adapter barcodes, as time/memory use is exponential. 183s samplerate=1 Set lower to only process a fraction of input reads. 183s samref= Optional reference fasta for processing sam files. 183s 183s Output parameters: 183s out= (outnonmatch) Write reads here that do not contain 183s kmers matching the database. 'out=stdout.fq' will pipe 183s to standard out. 183s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 183s different file. 183s outm= (outmatch) Write reads here that fail filters. In default 183s kfilter mode, this means any read with a matching kmer. 183s In any mode, it also includes reads that fail filters such 183s as minlength, mingc, maxgc, entropy, etc. In other words, 183s it includes all reads that do not go to 'out'. 183s outm2= (outmatch2) Use this to write 2nd read of pairs to a 183s different file. 183s outs= (outsingle) Use this to write singleton reads whose mate 183s was trimmed shorter than minlen. 183s stats= Write statistics about which contamininants were detected. 183s refstats= Write statistics on a per-reference-file basis. 183s rpkm= Write RPKM for each reference sequence (for RNA-seq). 183s dump= Dump kmer tables to a file, in fasta format. 183s duk= Write statistics in duk's format. *DEPRECATED* 183s nzo=t Only write statistics about ref sequences with nonzero hits. 183s overwrite=t (ow) Grant permission to overwrite files. 183s showspeed=t (ss) 'f' suppresses display of processing speed. 183s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 183s fastawrap=70 Length of lines in fasta output. 183s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 183s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 183s 5 includes base counts. 183s rename=f Rename reads to indicate which sequences they matched. 183s refnames=f Use names of reference files rather than scaffold IDs. 183s trd=f Truncate read and ref names at the first whitespace. 183s ordered=f Set to true to output reads in same order as input. 183s maxbasesout=-1 If positive, quit after writing approximately this many 183s bases to out (outu/outnonmatch). 183s maxbasesoutm=-1 If positive, quit after writing approximately this many 183s bases to outm (outmatch). 183s json=f Print to screen in json format. 183s 183s Histogram output parameters: 183s bhist= Base composition histogram by position. 183s qhist= Quality histogram by position. 183s qchist= Count of bases with each quality value. 183s aqhist= Histogram of average read quality. 183s bqhist= Quality histogram designed for box plots. 183s lhist= Read length histogram. 183s phist= Polymer length histogram. 183s gchist= Read GC content histogram. 183s enthist= Read entropy histogram. 183s ihist= Insert size histogram, for paired reads in mapped sam. 183s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 183s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 183s more memory. The default is 6000 for some histograms 183s and 80000 for others. 183s 183s Histograms for mapped sam/bam files only: 183s histbefore=t Calculate histograms from reads before processing. 183s ehist= Errors-per-read histogram. 183s qahist= Quality accuracy histogram of error rates versus quality 183s score. 183s indelhist= Indel length histogram. 183s mhist= Histogram of match, sub, del, and ins rates by position. 183s idhist= Histogram of read count versus percent identity. 183s idbins=100 Number idhist bins. Set to 'auto' to use read length. 183s varfile= Ignore substitution errors listed in this file when 183s calculating error rates. Can be generated with 183s CallVariants. 183s vcf= Ignore substitution errors listed in this VCF file 183s when calculating error rates. 183s ignorevcfindels=t Also ignore indels listed in the VCF. 183s 183s Processing parameters: 183s k=27 Kmer length used for finding contaminants. Contaminants 183s shorter than k will not be found. k must be at least 1. 183s rcomp=t Look for reverse-complements of kmers in addition to 183s forward kmers. 183s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 183s increase sensitivity in the presence of errors. This may 183s also be set to a number, e.g. mm=3, to mask that many bp. 183s The default mm=t corresponds to mm=1 for odd-length kmers 183s and mm=2 for even-length kmers (as of v39.04), while 183s mm=f is always equivalent to mm=0. 183s minkmerhits=1 (mkh) Reads need at least this many matching kmers 183s to be considered as matching the reference. 183s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 183s kmers to hit a ref, in order to be considered a match. 183s If this and minkmerhits are set, the greater is used. 183s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 183s bases to be covered by ref kmers to be considered a match. 183s If specified, mcf overrides mkh and mkf. 183s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 183s Memory use is proportional to (3*K)^hdist. 183s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 183s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 183s and indels). Memory use is proportional to (8*K)^edist. 183s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 183s qhdist2=0 Sets qhdist for short kmers, when using mink. 183s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 183s forbidn=f (fn) Forbids matching of read kmers containing N. 183s By default, these will match a reference 'A' if 183s hdist>0 or edist>0, to increase sensitivity. 183s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 183s match (or either is trimmed shorter than minlen). 183s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 183s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 183s Set to false to require both. 183s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 183s This makes the statistics a bit odd. 183s findbestmatch=f (fbm) If multiple matches, associate read with sequence 183s sharing most kmers. Reduces speed. 183s skipr1=f Don't do kmer-based operations on read 1. 183s skipr2=f Don't do kmer-based operations on read 2. 183s ecco=f For overlapping paired reads only. Performs error- 183s correction with BBMerge prior to kmer operations. 183s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 183s matrices generated by CalcTrueQuality. 183s sam= If recalibration is desired, and matrices have not already 183s been generated, BBDuk will create them from the sam file. 183s amino=f Run in amino acid mode. Some features have not been 183s tested, but kmer-matching works fine. Maximum k is 12. 183s 183s Speed and Memory parameters: 183s threads=auto (t) Set number of threads to use; default is number of 183s logical processors. 183s prealloc=f Preallocate memory in table. Allows faster table loading 183s and more efficient memory usage, for a large reference. 183s monitor=f Kill this process if it crashes. monitor=600,0.01 would 183s kill after 600 seconds under 1% usage. 183s minrskip=1 (mns) Force minimal skip interval when indexing reference 183s kmers. 1 means use all, 2 means use every other kmer, etc. 183s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 183s reference kmers. Normally all are used for scaffolds<100kb, 183s but with longer scaffolds, up to maxrskip-1 are skipped. 183s rskip= Set both minrskip and maxrskip to the same value. 183s If not set, rskip will vary based on sequence length. 183s qskip=1 Skip query kmers to increase speed. 1 means use all. 183s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 183s reads and reference. Increases speed and reduces memory. 183s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 183s 183s Trimming/Filtering/Masking parameters: 183s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 183s All kmer processing modes are mutually exclusive. 183s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 183s 183s ktrim=f Trim reads to remove bases matching reference kmers, plus 183s all bases to the left or right. 183s Values: 183s f (don't trim), 183s r (trim to the right), 183s l (trim to the left) 183s ktrimtips=0 Set this to a positive number to perform ktrim on both 183s ends, examining only the outermost X bases. 183s kmask= Replace bases matching ref kmers with another symbol. 183s Allows any non-whitespace character, and processes short 183s kmers on both ends if mink is set. 'kmask=lc' will 183s convert masked bases to lowercase. 183s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 183s ksplit=f For single-ended reads only. Reads will be split into 183s pairs around the kmer. If the kmer is at the end of the 183s read, it will be trimmed instead. Singletons will go to 183s out, and pairs will go to outm. Do not use ksplit with 183s other operations such as quality-trimming or filtering. 183s mink=0 Look for shorter kmers at read tips down to this length, 183s when k-trimming or masking. 0 means disabled. Enabling 183s this will disable maskmiddle. 183s qtrim=f Trim read ends to remove bases with quality below trimq. 183s Performed AFTER looking for kmers. Values: 183s rl (trim both ends), 183s f (neither end), 183s r (right end only), 183s l (left end only), 183s w (sliding window). 183s trimq=6 Regions with average quality BELOW this will be trimmed, 183s if qtrim is set to something other than f. Can be a 183s floating-point number like 7.3. 183s trimclip=f Trim soft-clipped bases from sam files. 183s minlength=10 (ml) Reads shorter than this after trimming will be 183s discarded. Pairs will be discarded if both are shorter. 183s mlf=0 (minlengthfraction) Reads shorter than this fraction of 183s original length after trimming will be discarded. 183s maxlength= Reads longer than this after trimming will be discarded. 183s minavgquality=0 (maq) Reads with average quality (after trimming) below 183s this will be discarded. 183s maqb=0 If positive, calculate maq from this many initial bases. 183s minbasequality=0 (mbq) Reads with any base below this quality (after 183s trimming) will be discarded. 183s maxns=-1 If non-negative, reads with more Ns than this 183s (after trimming) will be discarded. 183s mcb=0 (minconsecutivebases) Discard reads without at least 183s this many consecutive called bases. 183s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 183s than minlength to outm rather than discarding. 183s tp=0 (trimpad) Trim this much extra around matching kmers. 183s tbo=f (trimbyoverlap) Trim adapters based on where paired 183s reads overlap. 183s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 183s minoverlap=14 Require this many bases of overlap for detection. 183s mininsert=40 Require insert size of at least this for overlap. 183s Should be reduced to 16 for small RNA sequencing. 183s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 183s reads to the minimum length of either. 183s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 183s (exclusive, 0-based). 183s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 183s (exclusive, 0-based). 183s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 183s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 183s modulo this number. 183s restrictleft=0 If positive, only look for kmer matches in the 183s leftmost X bases. 183s restrictright=0 If positive, only look for kmer matches in the 183s rightmost X bases. 183s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 183s both ends is desired, use ktrimtips. 183s mingc=0 Discard reads with GC content below this. 183s maxgc=1 Discard reads with GC content above this. 183s gcpairs=t Use average GC of paired reads. 183s Also affects gchist. 183s tossjunk=f Discard reads with invalid characters as bases. 183s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 183s 183s Header-parsing parameters - these require Illumina headers: 183s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 183s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 183s or barcodes containing 'N' otherwise. A barcode must be 183s the last part of the read header. Values: 183s t: Remove reads with bad barcodes. 183s f: Ignore barcodes. 183s crash: Crash upon encountering bad barcodes. 183s barcodes= Comma-delimited list of barcodes or files of barcodes. 183s xmin=-1 If positive, discard reads with a lesser X coordinate. 183s ymin=-1 If positive, discard reads with a lesser Y coordinate. 183s xmax=-1 If positive, discard reads with a greater X coordinate. 183s ymax=-1 If positive, discard reads with a greater Y coordinate. 183s 183s Polymer trimming: 183s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 183s at least this length on either end of reads. 183s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 183s length on the left end of reads. Does not trim poly-C. 183s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 183s length on the right end of reads. Does not trim poly-C. 183s trimpolyg=0 This sets both left and right at once. 183s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 183s at least this length (on the left). 183s Note: there are also equivalent poly-C flags. 183s 183s Polymer tracking: 183s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 183s plen=20 Length of homopolymers to count. 183s 183s Entropy/Complexity parameters: 183s entropy=-1 Set between 0 and 1 to filter reads with entropy below 183s that value. Higher is more stringent. 183s entropywindow=50 Calculate entropy using a sliding window of this length. 183s entropyk=5 Calculate entropy using kmers of this length. 183s minbasefrequency=0 Discard reads with a minimum base frequency below this. 183s entropytrim=f Values: 183s f: (false) Do not entropy-trim. 183s r: (right) Trim low entropy on the right end only. 183s l: (left) Trim low entropy on the left end only. 183s rl: (both) Trim low entropy on both ends. 183s entropymask=f Values: 183s f: (filter) Discard low-entropy sequences. 183s t: (true) Mask low-entropy parts of sequences with N. 183s lc: Change low-entropy parts of sequences to lowercase. 183s entropymark=f Mark each base with its entropy value. This is on a scale 183s of 0-41 and is reported as quality scores, so the output 183s should be fastq or fasta+qual. 183s NOTE: If set, entropytrim overrides entropymask. 183s 183s Cardinality estimation: 183s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 183s cardinalityout=f (loglogout) Count unique kmers in output reads. 183s loglogk=31 Use this kmer length for counting. 183s loglogbuckets=2048 Use this many buckets for counting. 183s khist= Kmer frequency histogram; plots number of kmers versus 183s kmer depth. This is approximate. 183s khistout= Kmer frequency histogram for output reads. 183s 183s Java Parameters: 183s 183s -Xmx This will set Java's memory usage, overriding autodetection. 183s -Xmx20g will 183s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 183s The max is typically 85% of physical memory. 183s -eoom This flag will cause the process to exit if an 183s out-of-memory exception occurs. Requires Java 8u92+. 183s -da Disable assertions. 183s 183s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 183s 183s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 183s 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 183s 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] 183s Version 39.06 183s 183s 0.017 seconds. 183s Initial: 183s Memory: max=1491m, total=1491m, free=1461m, used=30m 183s 183s Input is being processed as paired 183s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 183s Started output streams: 0.012 seconds. 183s Processing time: 0.003 seconds. 183s 183s Input: 8 reads 306 bases. 183s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 183s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 183s Result: 0 reads (0.00%) 0 bases (0.00%) 183s 183s Time: 0.017 seconds. 183s Reads Processed: 8 0.47k reads/sec 183s Bases Processed: 306 0.02m bases/sec 183s test -r out.fastq.gz 183s 183s # bbnorm 183s bbnorm.sh --version 183s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 183s java -ea -Xmx2844m -Xms2844m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 183s BBMap version 39.06 183s For help, please run the shellscript with no parameters, or look in /docs/. 183s bbnorm.sh --help 183s 183s Written by Brian Bushnell 183s Last modified October 19, 2017 183s 183s Description: Normalizes read depth based on kmer counts. 183s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 183s However, Tadpole has superior error-correction to BBNorm. 183s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 183s 183s Usage: bbnorm.sh in= out= outt= hist= 183s 183s Input parameters: 183s in=null Primary input. Use in2 for paired reads in a second file 183s in2=null Second input file for paired reads in two files 183s extra=null Additional files to use for input (generating hash table) but not for output 183s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 183s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 183s kmersample=1 Process every nth kmer, and skip the rest 183s readsample=1 Process every nth read, and skip the rest 183s 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. 183s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 183s 183s Output parameters: 183s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 183s outt= (outtoss) File for reads that were excluded from primary output 183s reads=-1 Only process this number of reads, then quit (-1 means all) 183s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 183s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 183s 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. 183s Default is false, to prevent confusion about how there can be 0-count kmers. 183s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 183s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 183s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 183s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 183s rename=f Rename reads based on their kmer depth. 183s 183s Hashing parameters: 183s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 183s 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. 183s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 183s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 183s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 183s 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. 183s prehashes=2 Number of hashes for prefilter. 183s prefilterbits=2 (pbits) Bits per cell in prefilter. 183s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 183s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 183s minq=6 Ignore kmers containing bases with quality below this 183s minprob=0.5 Ignore kmers with overall probability of correctness below this 183s 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. 183s 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. 183s 183s Normalization parameters: 183s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 183s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 183s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 183s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 183s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 183s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 183s 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. 183s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 183s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 183s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 183s 183s Error detection parameters: 183s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 183s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 183s tossbadreads=f (tbr) Throw away reads detected as containing errors. 183s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 183s 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. 183s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 183s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 183s 183s Error correction parameters: 183s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 183s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 183s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 183s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 183s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 183s eccmaxqual=127 Do not correct bases with quality above this value. 183s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 183s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 183s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 183s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 183s overlap=f (ecco) Error correct by read overlap. 183s 183s Depth binning parameters: 183s lowbindepth=10 (lbd) Cutoff for low depth bin. 183s highbindepth=80 (hbd) Cutoff for high depth bin. 183s outlow= Pairs in which both reads have a median below lbd go into this file. 183s outhigh= Pairs in which both reads have a median above hbd go into this file. 183s outmid= All other pairs go into this file. 183s 183s Histogram parameters: 183s hist= Specify a file to write the input kmer depth histogram. 183s histout= Specify a file to write the output kmer depth histogram. 183s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 183s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 183s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 183s 183s Peak calling parameters: 183s peaks= Write the peaks to this file. Default is stdout. 183s minHeight=2 (h) Ignore peaks shorter than this. 183s minVolume=5 (v) Ignore peaks with less area than this. 183s minWidth=3 (w) Ignore peaks narrower than this. 183s minPeak=2 (minp) Ignore peaks with an X-value below this. 183s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 183s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 183s 183s Java Parameters: 183s -Xmx This will set Java's memory usage, overriding autodetection. 183s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 183s The max is typically 85% of physical memory. 183s -eoom This flag will cause the process to exit if an 183s out-of-memory exception occurs. Requires Java 8u92+. 183s -da Disable assertions. 183s 183s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 183s 183s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 183s out=out3.fastq outt=outt.fastq hist=hist.plt 183s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 183s 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 183s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 183s 183s 183s *********** Pass 1 ********** 183s 183s 183s Settings: 183s threads: 4 183s k: 31 183s deterministic: true 183s toss error reads: false 183s passes: 1 183s bits per cell: 16 183s cells: 1052.92M 183s hashes: 3 183s base min quality: 5 183s kmer min prob: 0.5 183s 183s target depth: 400 183s min depth: 3 183s max depth: 500 183s min good kmers: 15 183s depth percentile: 64.8 183s ignore dupe kmers: true 183s fix spikes: false 183s histogram length: 65536 183s print zero cov: false 183s 185s Made hash table: hashes = 3 mem = 1.96 GB cells = 1052.59M used = 0.000% 185s 185s Estimated unique kmers: 7 185s 185s Table creation time: 1.569 seconds. 185s Started output threads. 185s Started output threads. 185s Table read time: 0.007 seconds. 28.10 kb/sec 185s Total reads in: 2 0.000% Kept 185s Total bases in: 188 0.000% Kept 185s Error reads in: 2 100.000% 185s Error type 1: 2 100.000% 185s Error type 2: 0 0.000% 185s Error type 3: 0 0.000% 185s 185s Wrote histogram to hist.plt 185s Total kmers counted: 128 185s Total unique kmer count: 128 185s Includes forward kmers only. 185s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 185s The most accurate value is the greater of the two. 185s 185s Percent unique: 100.00% 185s Depth average: 1.00 (unique kmers) 185s Depth median: 1 (unique kmers) 185s Depth standard deviation: 0.00 (unique kmers) 185s Corrected depth average: 0.00 185s 185s Depth average: 1.00 (all kmers) 185s Depth median: 1 (all kmers) 185s Depth standard deviation: 0.00 (all kmers) 185s 185s Approx. read depth median: 1.47 185s 185s *********** Pass 2 ********** 185s 185s 185s Settings: 185s threads: 4 185s k: 31 185s deterministic: true 185s toss error reads: false 185s passes: 1 185s bits per cell: 16 185s cells: 1052.92M 185s hashes: 3 185s base min quality: 5 185s kmer min prob: 0.5 185s 185s target depth: 100 185s min depth: 5 185s max depth: 100 185s min good kmers: 15 185s depth percentile: 54.0 185s ignore dupe kmers: true 185s fix spikes: false 185s histogram length: 65536 185s 185s Made hash table: hashes = 3 mem = 1.96 GB cells = 1052.59M used = 0.000% 185s 185s Estimated unique kmers: 0 185s 185s Table creation time: 0.668 seconds. 185s Started output threads. 185s Started output threads. 185s Table read time: 0.001 seconds. 0.00 kb/sec 185s Total reads in: 0 NaN% Kept 185s Total bases in: 0 NaN% Kept 185s Error reads in: 0 NaN% 185s Error type 1: 0 NaN% 185s Error type 2: 0 NaN% 185s Error type 3: 0 NaN% 185s Total kmers counted: 0 185s Total unique kmer count: 0 185s Includes forward kmers only. 185s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 185s The most accurate value is the greater of the two. 185s 185s Percent unique: NaN% 185s Depth average: NaN (unique kmers) 185s Depth median: 0 (unique kmers) 185s Depth standard deviation: NaN (unique kmers) 185s Corrected depth average: NaN 185s 185s Depth average: NaN (all kmers) 185s Depth median: 0 (all kmers) 185s Depth standard deviation: 0.00 (all kmers) 185s 185s Approx. read depth median: NaN 185s 185s Removing temp files. 185s 185s Total time: 2.325 seconds. 0.08 kb/sec 186s test -r out3.fastq 186s test -r outt.fastq 186s test -r hist.plt 186s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 186s out=out4.fastq outt=outt2.fastq hist=hist2.plt 186s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 186s java -ea -Xmx2845m -Xms2845m -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 186s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 186s 186s 186s *********** Pass 1 ********** 186s 186s 186s Settings: 186s threads: 4 186s k: 31 186s deterministic: true 186s toss error reads: false 186s passes: 1 186s bits per cell: 16 186s cells: 1053.69M 186s hashes: 3 186s base min quality: 5 186s kmer min prob: 0.5 186s 186s target depth: 400 186s min depth: 3 186s max depth: 500 186s min good kmers: 15 186s depth percentile: 64.8 186s ignore dupe kmers: true 186s fix spikes: false 186s histogram length: 65536 186s print zero cov: false 186s 187s Made hash table: hashes = 3 mem = 1.96 GB cells = 1053.64M used = 0.000% 187s 187s Estimated unique kmers: 7 187s 187s Table creation time: 1.163 seconds. 187s Started output threads. 187s Started output threads. 187s Table read time: 0.005 seconds. 25.90 kb/sec 187s Total reads in: 2 0.000% Kept 187s Total bases in: 126 0.000% Kept 187s Error reads in: 2 100.000% 187s Error type 1: 2 100.000% 187s Error type 2: 0 0.000% 187s Error type 3: 0 0.000% 187s 187s Wrote histogram to hist2.plt 187s Total kmers counted: 66 187s Total unique kmer count: 66 187s Includes forward kmers only. 187s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 187s The most accurate value is the greater of the two. 187s 187s Percent unique: 100.00% 187s Depth average: 1.00 (unique kmers) 187s Depth median: 1 (unique kmers) 187s Depth standard deviation: 0.00 (unique kmers) 187s Corrected depth average: 0.00 187s 187s Depth average: 1.00 (all kmers) 187s Depth median: 1 (all kmers) 187s Depth standard deviation: 0.00 (all kmers) 187s 187s Approx. read depth median: 1.91 187s 187s *********** Pass 2 ********** 187s 187s 187s Settings: 187s threads: 4 187s k: 31 187s deterministic: true 187s toss error reads: false 187s passes: 1 187s bits per cell: 16 187s cells: 1053.69M 187s hashes: 3 187s base min quality: 5 187s kmer min prob: 0.5 187s 187s target depth: 100 187s min depth: 5 187s max depth: 100 187s min good kmers: 15 187s depth percentile: 54.0 187s ignore dupe kmers: true 187s fix spikes: false 187s histogram length: 65536 187s 188s Made hash table: hashes = 3 mem = 1.96 GB cells = 1053.64M used = 0.000% 188s 188s Estimated unique kmers: 0 188s 188s Table creation time: 0.805 seconds. 188s Started output threads. 188s Started output threads. 188s Table read time: 0.002 seconds. 0.00 kb/sec 188s Total reads in: 0 NaN% Kept 188s Total bases in: 0 NaN% Kept 188s Error reads in: 0 NaN% 188s Error type 1: 0 NaN% 188s Error type 2: 0 NaN% 188s Error type 3: 0 NaN% 188s Total kmers counted: 0 188s Total unique kmer count: 0 188s Includes forward kmers only. 188s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 188s The most accurate value is the greater of the two. 188s 188s Percent unique: NaN% 188s Depth average: NaN (unique kmers) 188s Depth median: 0 (unique kmers) 188s Depth standard deviation: NaN (unique kmers) 188s Corrected depth average: NaN 188s 188s Depth average: NaN (all kmers) 188s Depth median: 0 (all kmers) 188s Depth standard deviation: 0.00 (all kmers) 188s 188s Approx. read depth median: NaN 188s 188s Removing temp files. 188s 188s Total time: 2.047 seconds. 0.06 kb/sec 188s test -r out4.fastq 188s test -r outt2.fastq 188s test -r hist2.plt 189s autopkgtest [01:03:54]: test run-unit-test: -----------------------] 189s autopkgtest [01:03:54]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 189s run-unit-test PASS 190s autopkgtest [01:03:55]: @@@@@@@@@@@@@@@@@@@@ summary 190s run-unit-test PASS 201s Creating nova instance adt-noble-s390x-bbmap-20240322-010045-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240321.img (UUID f7ee8f0f-480f-4014-94f0-3be2a19e259d)...