0s autopkgtest [07:46:25]: starting date and time: 2024-03-21 07:46:25+0000 0s autopkgtest [07:46:25]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [07:46:25]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7cqh2t14/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:openjdk-lts,src:alsa-lib,src:cups,src:gnutls28,src:libpng1.6,src:nettle,src:wp2latex --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-lts/11.0.23~7ea-1ubuntu1 alsa-lib/1.2.11-1build1 cups/2.4.7-1.2ubuntu1 gnutls28/3.8.3-1.1ubuntu2 libpng1.6/1.6.43-3 nettle/3.9.1-2.2 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-arm64-5.secgroup --name adt-noble-arm64-bbmap-20240321-074624-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 127s autopkgtest [07:48:32]: testbed dpkg architecture: arm64 127s autopkgtest [07:48:32]: testbed apt version: 2.7.12 127s autopkgtest [07:48:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 128s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 128s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [492 kB] 129s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 129s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 129s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3769 kB] 129s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [683 kB] 129s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 129s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [41.7 kB] 129s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 129s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4177 kB] 129s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 129s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [67.4 kB] 129s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 134s Fetched 9418 kB in 2s (4524 kB/s) 134s Reading package lists... 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 139s Calculating upgrade... 140s The following packages will be upgraded: 140s debianutils linux-firmware ubuntu-minimal ubuntu-standard 140s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Need to get 476 MB of archives. 140s After this operation, 5724 kB of additional disk space will be used. 140s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 debianutils arm64 5.17 [90.1 kB] 140s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536build1 [10.7 kB] 140s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536build1 [10.7 kB] 140s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 linux-firmware arm64 20240318.git3b128b60-0ubuntu1 [475 MB] 168s Fetched 476 MB in 28s (16.9 MB/s) 169s (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 ... 75850 files and directories currently installed.) 169s Preparing to unpack .../debianutils_5.17_arm64.deb ... 169s Unpacking debianutils (5.17) over (5.16) ... 169s Setting up debianutils (5.17) ... 169s (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 ... 75850 files and directories currently installed.) 169s Preparing to unpack .../ubuntu-minimal_1.536build1_arm64.deb ... 169s Unpacking ubuntu-minimal (1.536build1) over (1.536) ... 169s Preparing to unpack .../ubuntu-standard_1.536build1_arm64.deb ... 169s Unpacking ubuntu-standard (1.536build1) over (1.536) ... 169s Preparing to unpack .../linux-firmware_20240318.git3b128b60-0ubuntu1_arm64.deb ... 169s Unpacking linux-firmware (20240318.git3b128b60-0ubuntu1) over (20240202.git36777504-0ubuntu1) ... 173s Setting up ubuntu-minimal (1.536build1) ... 174s Setting up linux-firmware (20240318.git3b128b60-0ubuntu1) ... 174s Setting up ubuntu-standard (1.536build1) ... 174s Processing triggers for man-db (2.12.0-3) ... 174s Processing triggers for initramfs-tools (0.142ubuntu20) ... 174s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 174s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 193s System running in EFI mode, skipping. 194s Reading package lists... 194s Building dependency tree... 194s Reading state information... 195s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 196s sh: Attempting to set up Debian/Ubuntu apt sources automatically 196s sh: Distribution appears to be Ubuntu 198s Reading package lists... 198s Building dependency tree... 198s Reading state information... 199s eatmydata is already the newest version (131-1). 199s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 199s Reading package lists... 199s Building dependency tree... 199s Reading state information... 200s dbus is already the newest version (1.14.10-4ubuntu1). 200s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 200s Reading package lists... 201s Building dependency tree... 201s Reading state information... 202s rng-tools-debian is already the newest version (2.4). 202s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 202s Reading package lists... 202s Building dependency tree... 202s Reading state information... 203s The following packages will be REMOVED: 203s cloud-init* python3-configobj* python3-debconf* 204s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 204s After this operation, 3252 kB disk space will be freed. 204s (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 ... 75912 files and directories currently installed.) 204s Removing cloud-init (24.1.1-0ubuntu1) ... 205s Removing python3-configobj (5.0.8-3) ... 205s Removing python3-debconf (1.5.86) ... 205s Processing triggers for man-db (2.12.0-3) ... 206s (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 ... 75523 files and directories currently installed.) 206s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 207s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 207s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 207s invoke-rc.d: policy-rc.d denied execution of try-restart. 207s Reading package lists... 207s Building dependency tree... 207s Reading state information... 209s linux-generic is already the newest version (6.8.0-11.11+1). 209s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 209s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 209s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 209s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 214s Reading package lists... 214s Reading package lists... 214s Building dependency tree... 214s Reading state information... 215s Calculating upgrade... 216s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 216s Reading package lists... 216s Building dependency tree... 216s Reading state information... 217s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 218s autopkgtest [07:50:03]: rebooting testbed after setup commands that affected boot 367s autopkgtest [07:52:32]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 370s autopkgtest [07:52:35]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 373s Get:1 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (dsc) [2286 B] 373s Get:2 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (tar) [5343 kB] 373s Get:3 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (diff) [25.4 kB] 373s gpgv: Signature made Fri Nov 24 11:00:29 2023 UTC 373s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 373s gpgv: issuer "emollier@debian.org" 373s gpgv: Can't check signature: No public key 373s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.06+dfsg-1.dsc: no acceptable signature found 374s autopkgtest [07:52:39]: testing package bbmap version 39.06+dfsg-1 374s autopkgtest [07:52:39]: build not needed 420s autopkgtest [07:53:25]: test run-unit-test: preparing testbed 427s Reading package lists... 427s Building dependency tree... 427s Reading state information... 428s Starting pkgProblemResolver with broken count: 0 428s Starting 2 pkgProblemResolver with broken count: 0 428s Done 429s The following additional packages will be installed: 429s bbmap bbmap-jni ca-certificates-java fontconfig-config fonts-dejavu-core 429s fonts-dejavu-mono java-common libapache-pom-java libasound2 libasound2-data 429s libavahi-client3 libavahi-common-data libavahi-common3 libcommons-cli-java 429s libcommons-codec-java libcommons-io-java libcommons-parent-java libcups2 429s libfontconfig1 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 429s liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 429s python-biopython-doc 429s Suggested packages: 429s default-jre libasound2-plugins alsa-utils libcommons-io-java-doc cups-common 429s liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd libnss-mdns 429s fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 429s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 429s Recommended packages: 429s pigz alsa-ucm-conf alsa-topology-conf python3-biopython 429s The following NEW packages will be installed: 429s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java fontconfig-config 429s fonts-dejavu-core fonts-dejavu-mono java-common libapache-pom-java 429s libasound2 libasound2-data libavahi-client3 libavahi-common-data 429s libavahi-common3 libcommons-cli-java libcommons-codec-java 429s libcommons-io-java libcommons-parent-java libcups2 libfontconfig1 429s libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 liblcms2-2 429s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 429s python-biopython-doc 429s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 429s Need to get 79.2 MB/79.2 MB of archives. 429s After this operation, 238 MB of additional disk space will be used. 429s Get:1 /tmp/autopkgtest.FSZmEi/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 430s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-cli-java all 1.6.0-1 [59.9 kB] 430s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libapache-pom-java all 29-2 [5284 B] 430s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 430s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-codec-java all 1.16.0-1 [306 kB] 430s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-io-java all 2.11.0-2 [297 kB] 430s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 liblog4j1.2-java all 1.2.17-11 [439 kB] 430s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libmpj-java all 0.44+dfsg-4 [443 kB] 430s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates-java all 20240118 [11.6 kB] 430s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 java-common all 0.75+exp1 [6798 B] 430s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common-data arm64 0.8-13ubuntu2 [29.5 kB] 430s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common3 arm64 0.8-13ubuntu2 [23.2 kB] 430s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-client3 arm64 0.8-13ubuntu2 [27.3 kB] 430s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libcups2 arm64 2.4.6-0ubuntu3 [270 kB] 430s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 430s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 430s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 430s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 430s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 430s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 430s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 430s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2-data all 1.2.10-3build1 [20.7 kB] 430s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2 arm64 1.2.10-3build1 [386 kB] 430s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 430s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 430s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libpcsclite1 arm64 2.0.0-1 [21.2 kB] 430s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-17-jre-headless arm64 17.0.10+7-1 [47.3 MB] 431s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 bbmap all 39.06+dfsg-1 [9768 kB] 432s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 bbmap-jni arm64 39.06+dfsg-1 [26.3 kB] 432s Get:30 http://ftpmaster.internal/ubuntu noble/universe arm64 python-biopython-doc all 1.81+dfsg-3 [17.3 MB] 433s Fetched 79.2 MB in 3s (29.1 MB/s) 433s Selecting previously unselected package libcommons-cli-java. 433s (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 ... 75468 files and directories currently installed.) 433s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 433s Unpacking libcommons-cli-java (1.6.0-1) ... 433s Selecting previously unselected package libapache-pom-java. 433s Preparing to unpack .../01-libapache-pom-java_29-2_all.deb ... 433s Unpacking libapache-pom-java (29-2) ... 433s Selecting previously unselected package libcommons-parent-java. 433s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 433s Unpacking libcommons-parent-java (56-1) ... 433s Selecting previously unselected package libcommons-codec-java. 433s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 433s Unpacking libcommons-codec-java (1.16.0-1) ... 433s Selecting previously unselected package libcommons-io-java. 433s Preparing to unpack .../04-libcommons-io-java_2.11.0-2_all.deb ... 433s Unpacking libcommons-io-java (2.11.0-2) ... 433s Selecting previously unselected package liblog4j1.2-java. 433s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 433s Unpacking liblog4j1.2-java (1.2.17-11) ... 433s Selecting previously unselected package libmpj-java. 433s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 433s Unpacking libmpj-java (0.44+dfsg-4) ... 433s Selecting previously unselected package ca-certificates-java. 433s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 433s Unpacking ca-certificates-java (20240118) ... 433s Selecting previously unselected package java-common. 433s Preparing to unpack .../08-java-common_0.75+exp1_all.deb ... 433s Unpacking java-common (0.75+exp1) ... 433s Selecting previously unselected package libavahi-common-data:arm64. 433s Preparing to unpack .../09-libavahi-common-data_0.8-13ubuntu2_arm64.deb ... 433s Unpacking libavahi-common-data:arm64 (0.8-13ubuntu2) ... 433s Selecting previously unselected package libavahi-common3:arm64. 433s Preparing to unpack .../10-libavahi-common3_0.8-13ubuntu2_arm64.deb ... 433s Unpacking libavahi-common3:arm64 (0.8-13ubuntu2) ... 434s Selecting previously unselected package libavahi-client3:arm64. 434s Preparing to unpack .../11-libavahi-client3_0.8-13ubuntu2_arm64.deb ... 434s Unpacking libavahi-client3:arm64 (0.8-13ubuntu2) ... 434s Selecting previously unselected package libcups2:arm64. 434s Preparing to unpack .../12-libcups2_2.4.6-0ubuntu3_arm64.deb ... 434s Unpacking libcups2:arm64 (2.4.6-0ubuntu3) ... 434s Selecting previously unselected package liblcms2-2:arm64. 434s Preparing to unpack .../13-liblcms2-2_2.14-2_arm64.deb ... 434s Unpacking liblcms2-2:arm64 (2.14-2) ... 434s Selecting previously unselected package libjpeg-turbo8:arm64. 434s Preparing to unpack .../14-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 434s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 434s Selecting previously unselected package libjpeg8:arm64. 434s Preparing to unpack .../15-libjpeg8_8c-2ubuntu11_arm64.deb ... 434s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 434s Selecting previously unselected package fonts-dejavu-mono. 434s Preparing to unpack .../16-fonts-dejavu-mono_2.37-8_all.deb ... 434s Unpacking fonts-dejavu-mono (2.37-8) ... 434s Selecting previously unselected package fonts-dejavu-core. 434s Preparing to unpack .../17-fonts-dejavu-core_2.37-8_all.deb ... 434s Unpacking fonts-dejavu-core (2.37-8) ... 434s Selecting previously unselected package fontconfig-config. 434s Preparing to unpack .../18-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 434s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 434s Selecting previously unselected package libfontconfig1:arm64. 434s Preparing to unpack .../19-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 434s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 434s Selecting previously unselected package libasound2-data. 434s Preparing to unpack .../20-libasound2-data_1.2.10-3build1_all.deb ... 434s Unpacking libasound2-data (1.2.10-3build1) ... 434s Selecting previously unselected package libasound2:arm64. 434s Preparing to unpack .../21-libasound2_1.2.10-3build1_arm64.deb ... 434s Unpacking libasound2:arm64 (1.2.10-3build1) ... 434s Selecting previously unselected package libgraphite2-3:arm64. 434s Preparing to unpack .../22-libgraphite2-3_1.3.14-2_arm64.deb ... 434s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 434s Selecting previously unselected package libharfbuzz0b:arm64. 435s Preparing to unpack .../23-libharfbuzz0b_8.3.0-2_arm64.deb ... 435s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 435s Selecting previously unselected package libpcsclite1:arm64. 435s Preparing to unpack .../24-libpcsclite1_2.0.0-1_arm64.deb ... 435s Unpacking libpcsclite1:arm64 (2.0.0-1) ... 435s Selecting previously unselected package openjdk-17-jre-headless:arm64. 435s Preparing to unpack .../25-openjdk-17-jre-headless_17.0.10+7-1_arm64.deb ... 435s Unpacking openjdk-17-jre-headless:arm64 (17.0.10+7-1) ... 436s Selecting previously unselected package bbmap. 436s Preparing to unpack .../26-bbmap_39.06+dfsg-1_all.deb ... 436s Unpacking bbmap (39.06+dfsg-1) ... 436s Selecting previously unselected package bbmap-jni. 436s Preparing to unpack .../27-bbmap-jni_39.06+dfsg-1_arm64.deb ... 436s Unpacking bbmap-jni (39.06+dfsg-1) ... 436s Selecting previously unselected package python-biopython-doc. 436s Preparing to unpack .../28-python-biopython-doc_1.81+dfsg-3_all.deb ... 436s Unpacking python-biopython-doc (1.81+dfsg-3) ... 437s Selecting previously unselected package autopkgtest-satdep. 437s Preparing to unpack .../29-1-autopkgtest-satdep.deb ... 437s Unpacking autopkgtest-satdep (0) ... 437s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 437s Setting up liblcms2-2:arm64 (2.14-2) ... 437s Setting up java-common (0.75+exp1) ... 437s Setting up libcommons-cli-java (1.6.0-1) ... 437s Setting up liblog4j1.2-java (1.2.17-11) ... 437s Setting up libasound2-data (1.2.10-3build1) ... 437s Setting up libapache-pom-java (29-2) ... 437s Setting up libavahi-common-data:arm64 (0.8-13ubuntu2) ... 437s Setting up fonts-dejavu-mono (2.37-8) ... 437s Setting up fonts-dejavu-core (2.37-8) ... 437s Setting up libpcsclite1:arm64 (2.0.0-1) ... 437s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 437s Setting up python-biopython-doc (1.81+dfsg-3) ... 437s Setting up libasound2:arm64 (1.2.10-3build1) ... 437s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 437s Setting up bbmap-jni (39.06+dfsg-1) ... 437s Setting up ca-certificates-java (20240118) ... 437s No JRE found. Skipping Java certificates setup. 437s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 437s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 437s Setting up libcommons-parent-java (56-1) ... 437s Setting up libavahi-common3:arm64 (0.8-13ubuntu2) ... 437s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 437s Setting up libcommons-codec-java (1.16.0-1) ... 437s Setting up libavahi-client3:arm64 (0.8-13ubuntu2) ... 437s Setting up libcommons-io-java (2.11.0-2) ... 437s Setting up libmpj-java (0.44+dfsg-4) ... 437s Setting up libcups2:arm64 (2.4.6-0ubuntu3) ... 437s Setting up openjdk-17-jre-headless:arm64 (17.0.10+7-1) ... 437s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode 437s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 437s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 437s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 437s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 437s Processing triggers for libc-bin (2.39-0ubuntu2) ... 437s Processing triggers for man-db (2.12.0-3) ... 439s Processing triggers for ca-certificates-java (20240118) ... 439s Adding debian:ACCVRAIZ1.pem 439s Adding debian:AC_RAIZ_FNMT-RCM.pem 439s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 439s Adding debian:ANF_Secure_Server_Root_CA.pem 439s Adding debian:Actalis_Authentication_Root_CA.pem 439s Adding debian:AffirmTrust_Commercial.pem 439s Adding debian:AffirmTrust_Networking.pem 439s Adding debian:AffirmTrust_Premium.pem 439s Adding debian:AffirmTrust_Premium_ECC.pem 439s Adding debian:Amazon_Root_CA_1.pem 439s Adding debian:Amazon_Root_CA_2.pem 439s Adding debian:Amazon_Root_CA_3.pem 439s Adding debian:Amazon_Root_CA_4.pem 439s Adding debian:Atos_TrustedRoot_2011.pem 439s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 439s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 439s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 439s Adding debian:BJCA_Global_Root_CA1.pem 439s Adding debian:BJCA_Global_Root_CA2.pem 439s Adding debian:Baltimore_CyberTrust_Root.pem 439s Adding debian:Buypass_Class_2_Root_CA.pem 439s Adding debian:Buypass_Class_3_Root_CA.pem 439s Adding debian:CA_Disig_Root_R2.pem 439s Adding debian:CFCA_EV_ROOT.pem 439s Adding debian:COMODO_Certification_Authority.pem 439s Adding debian:COMODO_ECC_Certification_Authority.pem 439s Adding debian:COMODO_RSA_Certification_Authority.pem 439s Adding debian:Certainly_Root_E1.pem 439s Adding debian:Certainly_Root_R1.pem 439s Adding debian:Certigna.pem 439s Adding debian:Certigna_Root_CA.pem 439s Adding debian:Certum_EC-384_CA.pem 439s Adding debian:Certum_Trusted_Network_CA.pem 439s Adding debian:Certum_Trusted_Network_CA_2.pem 439s Adding debian:Certum_Trusted_Root_CA.pem 439s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 439s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 439s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 439s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 439s Adding debian:Comodo_AAA_Services_root.pem 439s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 439s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 439s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 439s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 439s Adding debian:DigiCert_Assured_ID_Root_CA.pem 439s Adding debian:DigiCert_Assured_ID_Root_G2.pem 439s Adding debian:DigiCert_Assured_ID_Root_G3.pem 439s Adding debian:DigiCert_Global_Root_CA.pem 439s Adding debian:DigiCert_Global_Root_G2.pem 439s Adding debian:DigiCert_Global_Root_G3.pem 439s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 439s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 439s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 439s Adding debian:DigiCert_Trusted_Root_G4.pem 439s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 439s Adding debian:Entrust_Root_Certification_Authority.pem 439s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 439s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 439s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 439s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 439s Adding debian:GLOBALTRUST_2020.pem 439s Adding debian:GTS_Root_R1.pem 439s Adding debian:GTS_Root_R2.pem 439s Adding debian:GTS_Root_R3.pem 439s Adding debian:GTS_Root_R4.pem 439s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 439s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 439s Adding debian:GlobalSign_Root_CA.pem 439s Adding debian:GlobalSign_Root_CA_-_R3.pem 439s Adding debian:GlobalSign_Root_CA_-_R6.pem 439s Adding debian:GlobalSign_Root_E46.pem 439s Adding debian:GlobalSign_Root_R46.pem 439s Adding debian:Go_Daddy_Class_2_CA.pem 439s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 439s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 439s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 440s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 440s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 440s Adding debian:HiPKI_Root_CA_-_G1.pem 440s Adding debian:Hongkong_Post_Root_CA_3.pem 440s Adding debian:ISRG_Root_X1.pem 440s Adding debian:ISRG_Root_X2.pem 440s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 440s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 440s Adding debian:Izenpe.com.pem 440s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 440s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 440s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 440s Adding debian:NAVER_Global_Root_Certification_Authority.pem 440s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 440s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 440s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 440s Adding debian:QuoVadis_Root_CA_1_G3.pem 440s Adding debian:QuoVadis_Root_CA_2.pem 440s Adding debian:QuoVadis_Root_CA_2_G3.pem 440s Adding debian:QuoVadis_Root_CA_3.pem 440s Adding debian:QuoVadis_Root_CA_3_G3.pem 440s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 440s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 440s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 440s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 440s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 440s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 440s Adding debian:SZAFIR_ROOT_CA2.pem 440s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 440s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 440s Adding debian:SecureSign_RootCA11.pem 440s Adding debian:SecureTrust_CA.pem 440s Adding debian:Secure_Global_CA.pem 440s Adding debian:Security_Communication_ECC_RootCA1.pem 440s Adding debian:Security_Communication_RootCA2.pem 440s Adding debian:Security_Communication_RootCA3.pem 440s Adding debian:Security_Communication_Root_CA.pem 440s Adding debian:Starfield_Class_2_CA.pem 440s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 440s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 440s Adding debian:SwissSign_Gold_CA_-_G2.pem 440s Adding debian:SwissSign_Silver_CA_-_G2.pem 440s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 440s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 440s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 440s Adding debian:TWCA_Global_Root_CA.pem 440s Adding debian:TWCA_Root_Certification_Authority.pem 440s Adding debian:TeliaSonera_Root_CA_v1.pem 440s Adding debian:Telia_Root_CA_v2.pem 440s Adding debian:TrustAsia_Global_Root_CA_G3.pem 440s Adding debian:TrustAsia_Global_Root_CA_G4.pem 440s Adding debian:Trustwave_Global_Certification_Authority.pem 440s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 440s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 440s Adding debian:TunTrust_Root_CA.pem 440s Adding debian:UCA_Extended_Validation_Root.pem 440s Adding debian:UCA_Global_G2_Root.pem 440s Adding debian:USERTrust_ECC_Certification_Authority.pem 440s Adding debian:USERTrust_RSA_Certification_Authority.pem 440s Adding debian:XRamp_Global_CA_Root.pem 440s Adding debian:certSIGN_ROOT_CA.pem 440s Adding debian:certSIGN_Root_CA_G2.pem 440s Adding debian:e-Szigno_Root_CA_2017.pem 440s Adding debian:ePKI_Root_Certification_Authority.pem 440s Adding debian:emSign_ECC_Root_CA_-_C3.pem 440s Adding debian:emSign_ECC_Root_CA_-_G3.pem 440s Adding debian:emSign_Root_CA_-_C1.pem 440s Adding debian:emSign_Root_CA_-_G1.pem 440s Adding debian:vTrus_ECC_Root_CA.pem 440s Adding debian:vTrus_Root_CA.pem 440s done. 440s Setting up bbmap (39.06+dfsg-1) ... 440s Setting up autopkgtest-satdep (0) ... 445s (Reading database ... 78313 files and directories currently installed.) 445s Removing autopkgtest-satdep (0) ... 446s autopkgtest [07:53:51]: test run-unit-test: [----------------------- 446s 446s # bbmap 446s bbmap.sh --version 446s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 446s java -ea -Xmx2799m -Xms2799m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 446s BBMap version 39.06 446s For help, please run the shellscript with no parameters, or look in /docs/. 446s bbmap.sh --help 446s 446s BBMap 446s Written by Brian Bushnell, from Dec. 2010 - present 446s Last modified September 15, 2022 446s 446s Description: Fast and accurate splice-aware read aligner. 446s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 446s 446s To index: bbmap.sh ref= 446s To map: bbmap.sh in= out= 446s To map without writing an index: 446s bbmap.sh ref= in= out= nodisk 446s 446s in=stdin will accept reads from standard in, and out=stdout will write to 446s standard out, but file extensions are still needed to specify the format of the 446s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 446s standard in; out=stdout.sam.gz will write gzipped sam. 446s 446s Indexing Parameters (required when building the index): 446s nodisk=f Set to true to build index in memory and write nothing 446s to disk except output. 446s ref= Specify the reference sequence. Only do this ONCE, 446s when building the index (unless using 'nodisk'). 446s build=1 If multiple references are indexed in the same directory, 446s each needs a unique numeric ID (unless using 'nodisk'). 446s k=13 Kmer length, range 8-15. Longer is faster but uses 446s more memory. Shorter is more sensitive. 446s If indexing and mapping are done in two steps, K should 446s be specified each time. 446s path=<.> Specify the location to write the index, if you don't 446s want it in the current working directory. 446s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 446s number (reduces RAM by 50% and sensitivity slightly). 446s Should be enabled both when building the index AND 446s when mapping. 446s rebuild=f Force a rebuild of the index (ref= should be set). 446s 446s Input Parameters: 446s build=1 Designate index to use. Corresponds to the number 446s specified when building the index. 446s in= Primary reads input; required parameter. 446s in2= For paired reads in two files. 446s interleaved=auto True forces paired/interleaved input; false forces 446s single-ended mapping. If not specified, interleaved 446s status will be autodetected from read names. 446s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 446s BBMap and 6000 for BBMapPacBio. Only works for FASTA 446s input (use 'maxlen' for FASTQ input). The default for 446s bbmap.sh is 500, and for mapPacBio.sh is 6000. 446s unpigz=f Spawn a pigz (parallel gzip) process for faster 446s decompression than using Java. 446s Requires pigz to be installed. 446s touppercase=t (tuc) Convert lowercase letters in reads to upper case 446s (otherwise they will not match the reference). 446s 446s Sampling Parameters: 446s 446s reads=-1 Set to a positive number N to only process the first N 446s reads (or pairs), then quit. -1 means use all reads. 446s samplerate=1 Set to a number from 0 to 1 to randomly select that 446s fraction of reads for mapping. 1 uses all reads. 446s skipreads=0 Set to a number N to skip the first N reads (or pairs), 446s then map the rest. 446s 446s Mapping Parameters: 446s fast=f This flag is a macro which sets other paramters to run 446s faster, at reduced sensitivity. Bad for RNA-seq. 446s slow=f This flag is a macro which sets other paramters to run 446s slower, at greater sensitivity. 'vslow' is even slower. 446s maxindel=16000 Don't look for indels longer than this. Lower is faster. 446s Set to >=100k for RNAseq with long introns like mammals. 446s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 446s By default these are not sought, but may be found anyway. 446s tipsearch=100 Look this far for read-end deletions with anchors 446s shorter than K, using brute force. 446s minid=0.76 Approximate minimum alignment identity to look for. 446s Higher is faster and less sensitive. 446s minhits=1 Minimum number of seed hits required for candidate sites. 446s Higher is faster. 446s local=f Set to true to use local, rather than global, alignments. 446s This will soft-clip ugly ends of poor alignments. 446s perfectmode=f Allow only perfect mappings when set to true (very fast). 446s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 446s N's in the reference) mappings. 446s threads=auto (t) Set to number of threads desired. By default, uses 446s all cores available. 446s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 446s multiple top-scoring mapping locations). 446s best (use the first best site) 446s toss (consider unmapped) 446s random (select one top-scoring site randomly) 446s all (retain all top-scoring sites) 446s samestrandpairs=f (ssp) Specify whether paired reads should map to the 446s same strand or opposite strands. 446s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 446s orientation. Set to false for long-mate-pair libraries. 446s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 446s insert size or orientation, the read with the lower 446s mapping quality is marked unmapped. 446s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 446s be sent to 'outu' but not 'outm'. 446s rcomp=f Reverse complement both reads prior to mapping (for LMP 446s outward-facing libraries). 446s rcompmate=f Reverse complement read2 prior to mapping. 446s pairlen=32000 Set max allowed distance between paired reads. 446s (insert size)=(pairlen)+(read1 length)+(read2 length) 446s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 446s greater than this. Lower is faster. 446s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 446s is faster. 446s averagepairdist=100 (apd) Initial average distance between paired reads. 446s Varies dynamically; does not need to be specified. 446s deterministic=f Run in deterministic mode. In this case it is good 446s to set averagepairdist. BBMap is deterministic 446s without this flag if using single-ended reads, 446s or run singlethreaded. 446s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 446s fraction of read length. Faster but less accurate. 446s bandwidth=0 (bw) Set the bandwidth directly. 446s fraction of read length. Faster but less accurate. 446s usejni=f (jni) Do alignments faster, in C code. Requires 446s compiling the C code; details are in /jni/README.txt. 446s maxsites2=800 Don't analyze (or print) more than this many alignments 446s per read. 446s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 446s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 446s will ignore the most common 3% of kmers. 446s greedy=t Use a greedy algorithm to discard the least-useful 446s kmers on a per-read basis. 446s kfilter=0 If positive, potential mapping sites must have at 446s least this many consecutive exact matches. 446s 446s 446s Quality and Trimming Parameters: 446s qin=auto Set to 33 or 64 to specify input quality value ASCII 446s offset. 33 is Sanger, 64 is old Solexa. 446s qout=auto Set to 33 or 64 to specify output quality value ASCII 446s offset (only if output format is fastq). 446s qtrim=f Quality-trim ends before mapping. Options are: 446s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 446s untrim=f Undo trimming after mapping. Untrimmed bases will be 446s soft-clipped in cigar strings. 446s trimq=6 Trim regions with average quality below this 446s (phred algorithm). 446s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 446s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 446s quality strings for fasta input reads. 446s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 446s out-of-range quality values. 446s usequality=t Use quality scores when determining which read kmers 446s to use as seeds. 446s minaveragequality=0 (maq) Do not map reads with average quality bbmap.sh ref=example.fasta 446s below this. 446s maqb=0 If positive, calculate maq from this many initial bases. 446s 446s Output Parameters: 446s out= Write all reads to this file. 446s outu= Write only unmapped reads to this file. Does not 446s include unmapped paired reads with a mapped mate. 446s outm= Write only mapped reads to this file. Includes 446s unmapped paired reads with a mapped mate. 446s mappedonly=f If true, treats 'out' like 'outm'. 446s bamscript= (bs) Write a shell script to that will turn 446s the sam output into a sorted, indexed bam file. 446s ordered=f Set to true to output reads in same order as input. 446s Slower and uses more memory. 446s overwrite=f (ow) Allow process to overwrite existing files. 446s secondary=f Print secondary alignments. 446s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 446s with score of at least this fraction of primary. 446s ssao=f (secondarysiteasambiguousonly) Only print secondary 446s alignments for ambiguously-mapped reads. 446s maxsites=5 Maximum number of total alignments to print per read. 446s Only relevant when secondary=t. 446s quickmatch=f Generate cigar strings more quickly. 446s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 446s assuming that the remainder is a comment or description. 446s ziplevel=2 (zl) Compression level for zip or gzip output. 446s pigz=f Spawn a pigz (parallel gzip) process for faster 446s compression than Java. Requires pigz to be installed. 446s machineout=f Set to true to output statistics in machine-friendly 446s 'key=value' format. 446s printunmappedcount=f Print the total number of unmapped reads and bases. 446s If input is paired, the number will be of pairs 446s for which both reads are unmapped. 446s showprogress=0 If positive, print a '.' every X reads. 446s showprogress2=0 If positive, print the number of seconds since the 446s last progress update (instead of a '.'). 446s renamebyinsert=f Renames reads based on their mapped insert size. 446s 446s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 446s bloom=f Use a Bloom filter to ignore reads not sharing kmers 446s with the reference. This uses more memory, but speeds 446s mapping when most reads don't match the reference. 446s bloomhashes=2 Number of hash functions. 446s bloomminhits=3 Number of consecutive hits to be considered matched. 446s bloomk=31 Bloom filter kmer length. 446s bloomserial=t Use the serialized Bloom filter for greater loading 446s speed, if available. If not, generate and write one. 446s 446s Post-Filtering Parameters: 446s idfilter=0 Independant of minid; sets exact minimum identity 446s allowed for alignments to be printed. Range 0 to 1. 446s subfilter=-1 Ban alignments with more than this many substitutions. 446s insfilter=-1 Ban alignments with more than this many insertions. 446s delfilter=-1 Ban alignments with more than this many deletions. 446s indelfilter=-1 Ban alignments with more than this many indels. 446s editfilter=-1 Ban alignments with more than this many edits. 446s inslenfilter=-1 Ban alignments with an insertion longer than this. 446s dellenfilter=-1 Ban alignments with a deletion longer than this. 446s nfilter=-1 Ban alignments with more than this many ns. This 446s includes nocall, noref, and off scaffold ends. 446s 446s Sam flags and settings: 446s noheader=f Disable generation of header lines. 446s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 446s with = and X, or 1.3 to use M. 446s saa=t (secondaryalignmentasterisks) Use asterisks instead of 446s bases for sam secondary alignments. 446s cigar=t Set to 'f' to skip generation of cigar strings (faster). 446s keepnames=f Keep original names of paired reads, rather than 446s ensuring both reads have the same name. 446s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 446s cigar strings for deletions of at least that length. 446s rgid= Set readgroup ID. All other readgroup fields 446s can be set similarly, with the flag rgXX= 446s If you set a readgroup flag to the word 'filename', 446s e.g. rgid=filename, the input file name will be used. 446s mdtag=f Write MD tags. 446s nhtag=f Write NH tags. 446s xmtag=f Write XM tags (may only work correctly with ambig=all). 446s amtag=f Write AM tags. 446s nmtag=f Write NM tags. 446s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 446s for RNAseq using firststrand, secondstrand, or 446s unstranded libraries. Needed by Cufflinks. 446s JGI mainly uses 'firststrand'. 446s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 446s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 446s prefixed by YL:Z: 446s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 446s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 446s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 446s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 446s boundstag=f Write a tag indicating whether either read in the pair 446s goes off the end of the reference, prefixed by XB:Z: 446s notags=f Turn off all optional tags. 446s 446s Histogram and statistics output parameters: 446s scafstats= Statistics on how many reads mapped to which scaffold. 446s refstats= Statistics on how many reads mapped to which reference 446s file; only for BBSplit. 446s sortscafs=t Sort scaffolds or references by read count. 446s bhist= Base composition histogram by position. 446s qhist= Quality histogram by position. 446s aqhist= Histogram of average read quality. 446s bqhist= Quality histogram designed for box plots. 446s lhist= Read length histogram. 446s ihist= Write histogram of insert sizes (for paired reads). 446s ehist= Errors-per-read histogram. 446s qahist= Quality accuracy histogram of error rates versus 446s quality score. 446s indelhist= Indel length histogram. 446s mhist= Histogram of match, sub, del, and ins rates by 446s read location. 446s gchist= Read GC content histogram. 446s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 446s gcpairs=t Use average GC of paired reads. 446s idhist= Histogram of read count versus percent identity. 446s idbins=100 Number idhist bins. Set to 'auto' to use read length. 446s statsfile=stderr Mapping statistics are printed here. 446s 446s Coverage output parameters (these may reduce speed and use more RAM): 446s covstats= Per-scaffold coverage info. 446s rpkm= Per-scaffold RPKM/FPKM counts. 446s covhist= Histogram of # occurrences of each depth level. 446s basecov= Coverage per base location. 446s bincov= Print binned coverage per location (one line per X bases). 446s covbinsize=1000 Set the binsize for binned coverage output. 446s nzo=t Only print scaffolds with nonzero coverage. 446s twocolumn=f Change to true to print only ID and Avg_fold instead of 446s all 6 columns to the 'out=' file. 446s 32bit=f Set to true if you need per-base coverage over 64k. 446s strandedcov=f Track coverage for plus and minus strand independently. 446s startcov=f Only track start positions of reads. 446s secondarycov=t Include coverage of secondary alignments. 446s physcov=f Calculate physical coverage for paired reads. 446s This includes the unsequenced bases. 446s delcoverage=t (delcov) Count bases covered by deletions as covered. 446s True is faster than false. 446s covk=0 If positive, calculate kmer coverage statistics. 446s 446s Java Parameters: 446s -Xmx This will set Java's memory usage, 446s overriding autodetection. 446s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 446s will specify 800 megs. The max is typically 85% of 446s physical memory. The human genome requires around 24g, 446s or 12g with the 'usemodulo' flag. The index uses 446s roughly 6 bytes per reference base. 446s -eoom This flag will cause the process to exit if an 446s out-of-memory exception occurs. Requires Java 8u92+. 446s -da Disable assertions. 446s 446s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 446s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 446s 446s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 446s java -ea -Xmx2799m -Xms2799m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 447s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 447s Version 39.06 447s 447s No output file. 447s Writing reference. 447s 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] 447s 447s Set genScaffoldInfo=true 447s Writing chunk 1 447s Set genome to 1 447s 447s Loaded Reference: 0.010 seconds. 447s Loading index for chunk 1-1, build 1 447s No index available; generating from reference genome: /tmp/autopkgtest.FSZmEi/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 447s Indexing threads started for block 0-1 447s Indexing threads finished for block 0-1 449s Generated Index: 2.115 seconds. 449s No reads to process; quitting. 449s 449s Total time: 2.374 seconds. 449s test -d ref 449s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 449s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 449s java -ea -Xmx2799m -Xms2799m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 449s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 449s Version 39.06 449s 449s Retaining first best site only for ambiguous mappings. 449s Set genome to 1 449s 449s Loaded Reference: 0.053 seconds. 449s Loading index for chunk 1-1, build 1 450s Generated Index: 0.712 seconds. 457s Analyzed Index: 6.867 seconds. 457s Started output stream: 0.044 seconds. 457s Cleared Memory: 0.119 seconds. 457s Processing reads in single-ended mode. 457s Started read stream. 457s Started 4 mapping threads. 457s Detecting finished threads: 0, 1, 2, 3 457s 457s ------------------ Results ------------------ 457s 457s Genome: 1 457s Key Length: 13 457s Max Indel: 16000 457s Minimum Score Ratio: 0.56 457s Mapping Mode: normal 457s Reads Used: 4 (153 bases) 457s 457s Mapping: 0.182 seconds. 457s Reads/sec: 21.94 457s kBases/sec: 0.84 457s 457s 457s Read 1 data: pct reads num reads pct bases num bases 457s 457s mapped: 0.0000% 0 0.0000% 0 457s unambiguous: 0.0000% 0 0.0000% 0 457s ambiguous: 0.0000% 0 0.0000% 0 457s low-Q discards: 25.0000% 1 19.6078% 30 457s 457s perfect best site: 0.0000% 0 0.0000% 0 457s semiperfect site: 0.0000% 0 0.0000% 0 457s 457s Match Rate: NA NA NaN% 0 457s Error Rate: NaN% 0 NaN% 0 457s Sub Rate: NaN% 0 NaN% 0 457s Del Rate: NaN% 0 NaN% 0 457s Ins Rate: NaN% 0 NaN% 0 457s N Rate: NaN% 0 NaN% 0 457s 457s Total time: 8.163 seconds. 457s test -r out.sam 457s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 458s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 458s java -ea -Xmx2799m -Xms2799m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 458s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 458s Version 39.06 458s 458s Retaining first best site only for ambiguous mappings. 458s 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] 458s 458s Set genScaffoldInfo=true 458s Set genome to 1 458s 458s Loaded Reference: 0.003 seconds. 458s Loading index for chunk 1-1, build 1 458s Indexing threads started for block 0-1 458s Indexing threads finished for block 0-1 458s Generated Index: 0.325 seconds. 465s Analyzed Index: 6.795 seconds. 465s Started output stream: 0.045 seconds. 465s Cleared Memory: 0.118 seconds. 465s Processing reads in single-ended mode. 465s Started read stream. 465s Started 4 mapping threads. 465s Detecting finished threads: 0, 1, 2, 3 465s 465s ------------------ Results ------------------ 465s 465s Genome: 1 465s Key Length: 13 465s Max Indel: 16000 465s Minimum Score Ratio: 0.56 465s Mapping Mode: normal 465s Reads Used: 3 (75 bases) 465s 465s Mapping: 0.193 seconds. 465s Reads/sec: 15.55 465s kBases/sec: 0.39 465s 465s 465s Read 1 data: pct reads num reads pct bases num bases 465s 465s mapped: 100.0000% 3 100.0000% 75 465s unambiguous: 100.0000% 3 100.0000% 75 465s ambiguous: 0.0000% 0 0.0000% 0 465s low-Q discards: 0.0000% 0 0.0000% 0 465s 465s perfect best site: 100.0000% 3 100.0000% 75 465s semiperfect site: 100.0000% 3 100.0000% 75 465s 465s Match Rate: NA NA 100.0000% 75 465s Error Rate: 0.0000% 0 0.0000% 0 465s Sub Rate: 0.0000% 0 0.0000% 0 465s Del Rate: 0.0000% 0 0.0000% 0 465s Ins Rate: 0.0000% 0 0.0000% 0 465s N Rate: 0.0000% 0 0.0000% 0 465s 465s Total time: 7.722 seconds. 465s test -r out2.sam 465s 465s # bbduk 465s bbduk.sh --version 466s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 466s java -ea -Xmx1399m -Xms1399m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 466s BBMap version 39.06 466s For help, please run the shellscript with no parameters, or look in /docs/. 466s bbduk.sh --help 466s 466s Written by Brian Bushnell 466s Last modified November 9, 2023 466s 466s Description: Compares reads to the kmers in a reference dataset, optionally 466s allowing an edit distance. Splits the reads into two outputs - those that 466s match the reference, and those that don't. Can also trim (remove) the matching 466s parts of the reads rather than binning the reads. 466s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 466s 466s Usage: bbduk.sh in= out= ref= 466s 466s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 466s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 466s fasta input, set in=stdin.fa.gz 466s 466s Input parameters: 466s in= Main input. in=stdin.fq will pipe from stdin. 466s in2= Input for 2nd read of pairs in a different file. 466s ref= Comma-delimited list of reference files. 466s In addition to filenames, you may also use the keywords: 466s adapters, artifacts, phix, lambda, pjet, mtst, kapa 466s literal= Comma-delimited list of literal reference sequences. 466s touppercase=f (tuc) Change all bases upper-case. 466s interleaved=auto (int) t/f overrides interleaved autodetection. 466s Must be set mainually when streaming fastq input. 466s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 466s reads=-1 If positive, quit after processing X reads or pairs. 466s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 466s possible unambiguous copies. Intended for short motifs 466s or adapter barcodes, as time/memory use is exponential. 466s samplerate=1 Set lower to only process a fraction of input reads. 466s samref= Optional reference fasta for processing sam files. 466s 466s Output parameters: 466s out= (outnonmatch) Write reads here that do not contain 466s kmers matching the database. 'out=stdout.fq' will pipe 466s to standard out. 466s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 466s different file. 466s outm= (outmatch) Write reads here that fail filters. In default 466s kfilter mode, this means any read with a matching kmer. 466s In any mode, it also includes reads that fail filters such 466s as minlength, mingc, maxgc, entropy, etc. In other words, 466s it includes all reads that do not go to 'out'. 466s outm2= (outmatch2) Use this to write 2nd read of pairs to a 466s different file. 466s outs= (outsingle) Use this to write singleton reads whose mate 466s was trimmed shorter than minlen. 466s stats= Write statistics about which contamininants were detected. 466s refstats= Write statistics on a per-reference-file basis. 466s rpkm= Write RPKM for each reference sequence (for RNA-seq). 466s dump= Dump kmer tables to a file, in fasta format. 466s duk= Write statistics in duk's format. *DEPRECATED* 466s nzo=t Only write statistics about ref sequences with nonzero hits. 466s overwrite=t (ow) Grant permission to overwrite files. 466s showspeed=t (ss) 'f' suppresses display of processing speed. 466s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 466s fastawrap=70 Length of lines in fasta output. 466s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 466s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 466s 5 includes base counts. 466s rename=f Rename reads to indicate which sequences they matched. 466s refnames=f Use names of reference files rather than scaffold IDs. 466s trd=f Truncate read and ref names at the first whitespace. 466s ordered=f Set to true to output reads in same order as input. 466s maxbasesout=-1 If positive, quit after writing approximately this many 466s bases to out (outu/outnonmatch). 466s maxbasesoutm=-1 If positive, quit after writing approximately this many 466s bases to outm (outmatch). 466s json=f Print to screen in json format. 466s 466s Histogram output parameters: 466s bhist= Base composition histogram by position. 466s qhist= Quality histogram by position. 466s qchist= Count of bases with each quality value. 466s aqhist= Histogram of average read quality. 466s bqhist= Quality histogram designed for box plots. 466s lhist= Read length histogram. 466s phist= Polymer length histogram. 466s gchist= Read GC content histogram. 466s enthist= Read entropy histogram. 466s ihist= Insert size histogram, for paired reads in mapped sam. 466s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 466s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 466s more memory. The default is 6000 for some histograms 466s and 80000 for others. 466s 466s Histograms for mapped sam/bam files only: 466s histbefore=t Calculate histograms from reads before processing. 466s ehist= Errors-per-read histogram. 466s qahist= Quality accuracy histogram of error rates versus quality 466s score. 466s indelhist= Indel length histogram. 466s mhist= Histogram of match, sub, del, and ins rates by position. 466s idhist= Histogram of read count versus percent identity. 466s idbins=100 Number idhist bins. Set to 'auto' to use read length. 466s varfile= Ignore substitution errors listed in this file when 466s calculating error rates. Can be generated with 466s CallVariants. 466s vcf= Ignore substitution errors listed in this VCF file 466s when calculating error rates. 466s ignorevcfindels=t Also ignore indels listed in the VCF. 466s 466s Processing parameters: 466s k=27 Kmer length used for finding contaminants. Contaminants 466s shorter than k will not be found. k must be at least 1. 466s rcomp=t Look for reverse-complements of kmers in addition to 466s forward kmers. 466s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 466s increase sensitivity in the presence of errors. This may 466s also be set to a number, e.g. mm=3, to mask that many bp. 466s The default mm=t corresponds to mm=1 for odd-length kmers 466s and mm=2 for even-length kmers (as of v39.04), while 466s mm=f is always equivalent to mm=0. 466s minkmerhits=1 (mkh) Reads need at least this many matching kmers 466s to be considered as matching the reference. 466s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 466s kmers to hit a ref, in order to be considered a match. 466s If this and minkmerhits are set, the greater is used. 466s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 466s bases to be covered by ref kmers to be considered a match. 466s If specified, mcf overrides mkh and mkf. 466s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 466s Memory use is proportional to (3*K)^hdist. 466s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 466s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 466s and indels). Memory use is proportional to (8*K)^edist. 466s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 466s qhdist2=0 Sets qhdist for short kmers, when using mink. 466s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 466s forbidn=f (fn) Forbids matching of read kmers containing N. 466s By default, these will match a reference 'A' if 466s hdist>0 or edist>0, to increase sensitivity. 466s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 466s match (or either is trimmed shorter than minlen). 466s Set to false to require both. 466s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 466s This makes the statistics a bit odd. 466s findbestmatch=f (fbm) If multiple matches, associate read with sequence 466s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 466s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 466s sharing most kmers. Reduces speed. 466s skipr1=f Don't do kmer-based operations on read 1. 466s skipr2=f Don't do kmer-based operations on read 2. 466s ecco=f For overlapping paired reads only. Performs error- 466s correction with BBMerge prior to kmer operations. 466s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 466s matrices generated by CalcTrueQuality. 466s sam= If recalibration is desired, and matrices have not already 466s been generated, BBDuk will create them from the sam file. 466s amino=f Run in amino acid mode. Some features have not been 466s tested, but kmer-matching works fine. Maximum k is 12. 466s 466s Speed and Memory parameters: 466s threads=auto (t) Set number of threads to use; default is number of 466s logical processors. 466s prealloc=f Preallocate memory in table. Allows faster table loading 466s and more efficient memory usage, for a large reference. 466s monitor=f Kill this process if it crashes. monitor=600,0.01 would 466s kill after 600 seconds under 1% usage. 466s minrskip=1 (mns) Force minimal skip interval when indexing reference 466s kmers. 1 means use all, 2 means use every other kmer, etc. 466s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 466s reference kmers. Normally all are used for scaffolds<100kb, 466s but with longer scaffolds, up to maxrskip-1 are skipped. 466s rskip= Set both minrskip and maxrskip to the same value. 466s If not set, rskip will vary based on sequence length. 466s qskip=1 Skip query kmers to increase speed. 1 means use all. 466s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 466s reads and reference. Increases speed and reduces memory. 466s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 466s 466s Trimming/Filtering/Masking parameters: 466s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 466s All kmer processing modes are mutually exclusive. 466s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 466s 466s ktrim=f Trim reads to remove bases matching reference kmers, plus 466s all bases to the left or right. 466s Values: 466s f (don't trim), 466s r (trim to the right), 466s l (trim to the left) 466s ktrimtips=0 Set this to a positive number to perform ktrim on both 466s ends, examining only the outermost X bases. 466s kmask= Replace bases matching ref kmers with another symbol. 466s Allows any non-whitespace character, and processes short 466s kmers on both ends if mink is set. 'kmask=lc' will 466s convert masked bases to lowercase. 466s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 466s ksplit=f For single-ended reads only. Reads will be split into 466s pairs around the kmer. If the kmer is at the end of the 466s read, it will be trimmed instead. Singletons will go to 466s out, and pairs will go to outm. Do not use ksplit with 466s other operations such as quality-trimming or filtering. 466s mink=0 Look for shorter kmers at read tips down to this length, 466s when k-trimming or masking. 0 means disabled. Enabling 466s this will disable maskmiddle. 466s qtrim=f Trim read ends to remove bases with quality below trimq. 466s Performed AFTER looking for kmers. Values: 466s rl (trim both ends), 466s f (neither end), 466s r (right end only), 466s l (left end only), 466s w (sliding window). 466s trimq=6 Regions with average quality BELOW this will be trimmed, 466s if qtrim is set to something other than f. Can be a 466s floating-point number like 7.3. 466s trimclip=f Trim soft-clipped bases from sam files. 466s minlength=10 (ml) Reads shorter than this after trimming will be 466s discarded. Pairs will be discarded if both are shorter. 466s mlf=0 (minlengthfraction) Reads shorter than this fraction of 466s original length after trimming will be discarded. 466s maxlength= Reads longer than this after trimming will be discarded. 466s minavgquality=0 (maq) Reads with average quality (after trimming) below 466s this will be discarded. 466s maqb=0 If positive, calculate maq from this many initial bases. 466s minbasequality=0 (mbq) Reads with any base below this quality (after 466s trimming) will be discarded. 466s maxns=-1 If non-negative, reads with more Ns than this 466s (after trimming) will be discarded. 466s mcb=0 (minconsecutivebases) Discard reads without at least 466s this many consecutive called bases. 466s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 466s than minlength to outm rather than discarding. 466s tp=0 (trimpad) Trim this much extra around matching kmers. 466s tbo=f (trimbyoverlap) Trim adapters based on where paired 466s reads overlap. 466s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 466s minoverlap=14 Require this many bases of overlap for detection. 466s mininsert=40 Require insert size of at least this for overlap. 466s Should be reduced to 16 for small RNA sequencing. 466s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 466s reads to the minimum length of either. 466s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 466s (exclusive, 0-based). 466s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 466s (exclusive, 0-based). 466s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 466s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 466s modulo this number. 466s restrictleft=0 If positive, only look for kmer matches in the 466s leftmost X bases. 466s restrictright=0 If positive, only look for kmer matches in the 466s rightmost X bases. 466s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 466s both ends is desired, use ktrimtips. 466s mingc=0 Discard reads with GC content below this. 466s maxgc=1 Discard reads with GC content above this. 466s gcpairs=t Use average GC of paired reads. 466s Also affects gchist. 466s tossjunk=f Discard reads with invalid characters as bases. 466s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 466s 466s Header-parsing parameters - these require Illumina headers: 466s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 466s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 466s or barcodes containing 'N' otherwise. A barcode must be 466s the last part of the read header. Values: 466s t: Remove reads with bad barcodes. 466s f: Ignore barcodes. 466s crash: Crash upon encountering bad barcodes. 466s barcodes= Comma-delimited list of barcodes or files of barcodes. 466s xmin=-1 If positive, discard reads with a lesser X coordinate. 466s ymin=-1 If positive, discard reads with a lesser Y coordinate. 466s xmax=-1 If positive, discard reads with a greater X coordinate. 466s ymax=-1 If positive, discard reads with a greater Y coordinate. 466s 466s Polymer trimming: 466s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 466s at least this length on either end of reads. 466s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 466s length on the left end of reads. Does not trim poly-C. 466s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 466s length on the right end of reads. Does not trim poly-C. 466s trimpolyg=0 This sets both left and right at once. 466s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 466s at least this length (on the left). 466s Note: there are also equivalent poly-C flags. 466s 466s Polymer tracking: 466s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 466s plen=20 Length of homopolymers to count. 466s 466s Entropy/Complexity parameters: 466s entropy=-1 Set between 0 and 1 to filter reads with entropy below 466s that value. Higher is more stringent. 466s entropywindow=50 Calculate entropy using a sliding window of this length. 466s entropyk=5 Calculate entropy using kmers of this length. 466s minbasefrequency=0 Discard reads with a minimum base frequency below this. 466s entropytrim=f Values: 466s f: (false) Do not entropy-trim. 466s r: (right) Trim low entropy on the right end only. 466s l: (left) Trim low entropy on the left end only. 466s rl: (both) Trim low entropy on both ends. 466s entropymask=f Values: 466s f: (filter) Discard low-entropy sequences. 466s t: (true) Mask low-entropy parts of sequences with N. 466s lc: Change low-entropy parts of sequences to lowercase. 466s entropymark=f Mark each base with its entropy value. This is on a scale 466s of 0-41 and is reported as quality scores, so the output 466s should be fastq or fasta+qual. 466s NOTE: If set, entropytrim overrides entropymask. 466s 466s Cardinality estimation: 466s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 466s cardinalityout=f (loglogout) Count unique kmers in output reads. 466s loglogk=31 Use this kmer length for counting. 466s loglogbuckets=2048 Use this many buckets for counting. 466s khist= Kmer frequency histogram; plots number of kmers versus 466s kmer depth. This is approximate. 466s khistout= Kmer frequency histogram for output reads. 466s 466s Java Parameters: 466s 466s -Xmx This will set Java's memory usage, overriding autodetection. 466s -Xmx20g will 466s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 466s The max is typically 85% of physical memory. 466s -eoom This flag will cause the process to exit if an 466s out-of-memory exception occurs. Requires Java 8u92+. 466s -da Disable assertions. 466s 466s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 466s 466s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 466s java -ea -Xmx1399m -Xms1399m -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 466s 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] 466s Version 39.06 466s 466s 0.030 seconds. 466s Initial: 466s Memory: max=1468m, total=1468m, free=1438m, used=30m 466s 466s Input is being processed as paired 466s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 466s Started output streams: 0.033 seconds. 466s Processing time: 0.007 seconds. 466s 466s Input: 8 reads 306 bases. 466s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 466s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 466s Result: 0 reads (0.00%) 0 bases (0.00%) 466s 466s Time: 0.044 seconds. 466s Reads Processed: 8 0.18k reads/sec 466s Bases Processed: 306 0.01m bases/sec 466s test -r out.fastq.gz 466s 466s # bbnorm 466s bbnorm.sh --version 466s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 466s java -ea -Xmx2799m -Xms2799m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 467s BBMap version 39.06 467s For help, please run the shellscript with no parameters, or look in /docs/. 467s bbnorm.sh --help 467s 467s Written by Brian Bushnell 467s Last modified October 19, 2017 467s 467s Description: Normalizes read depth based on kmer counts. 467s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 467s However, Tadpole has superior error-correction to BBNorm. 467s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 467s 467s Usage: bbnorm.sh in= out= outt= hist= 467s 467s Input parameters: 467s in=null Primary input. Use in2 for paired reads in a second file 467s in2=null Second input file for paired reads in two files 467s extra=null Additional files to use for input (generating hash table) but not for output 467s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 467s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 467s kmersample=1 Process every nth kmer, and skip the rest 467s readsample=1 Process every nth read, and skip the rest 467s 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. 467s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 467s 467s Output parameters: 467s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 467s outt= (outtoss) File for reads that were excluded from primary output 467s reads=-1 Only process this number of reads, then quit (-1 means all) 467s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 467s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 467s 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. 467s Default is false, to prevent confusion about how there can be 0-count kmers. 467s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 467s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 467s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 467s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 467s rename=f Rename reads based on their kmer depth. 467s 467s Hashing parameters: 467s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 467s 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. 467s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 467s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 467s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 467s 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. 467s prehashes=2 Number of hashes for prefilter. 467s prefilterbits=2 (pbits) Bits per cell in prefilter. 467s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 467s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 467s minq=6 Ignore kmers containing bases with quality below this 467s minprob=0.5 Ignore kmers with overall probability of correctness below this 467s 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. 467s 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. 467s 467s Normalization parameters: 467s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 467s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 467s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 467s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 467s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 467s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 467s 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. 467s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 467s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 467s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 467s 467s Error detection parameters: 467s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 467s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 467s tossbadreads=f (tbr) Throw away reads detected as containing errors. 467s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 467s 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. 467s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 467s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 467s 467s Error correction parameters: 467s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 467s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 467s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 467s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 467s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 467s eccmaxqual=127 Do not correct bases with quality above this value. 467s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 467s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 467s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 467s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 467s overlap=f (ecco) Error correct by read overlap. 467s 467s Depth binning parameters: 467s lowbindepth=10 (lbd) Cutoff for low depth bin. 467s highbindepth=80 (hbd) Cutoff for high depth bin. 467s outlow= Pairs in which both reads have a median below lbd go into this file. 467s outhigh= Pairs in which both reads have a median above hbd go into this file. 467s outmid= All other pairs go into this file. 467s 467s Histogram parameters: 467s hist= Specify a file to write the input kmer depth histogram. 467s histout= Specify a file to write the output kmer depth histogram. 467s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 467s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 467s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 467s 467s Peak calling parameters: 467s peaks= Write the peaks to this file. Default is stdout. 467s minHeight=2 (h) Ignore peaks shorter than this. 467s minVolume=5 (v) Ignore peaks with less area than this. 467s minWidth=3 (w) Ignore peaks narrower than this. 467s minPeak=2 (minp) Ignore peaks with an X-value below this. 467s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 467s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 467s 467s Java Parameters: 467s -Xmx This will set Java's memory usage, overriding autodetection. 467s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 467s The max is typically 85% of physical memory. 467s -eoom This flag will cause the process to exit if an 467s out-of-memory exception occurs. Requires Java 8u92+. 467s -da Disable assertions. 467s 467s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 467s 467s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 467s out=out3.fastq outt=outt.fastq hist=hist.plt 467s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 467s java -ea -Xmx2799m -Xms2799m -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 467s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 467s 467s 467s *********** Pass 1 ********** 467s 467s 467s Settings: 467s threads: 4 467s k: 31 467s deterministic: true 467s toss error reads: false 467s passes: 1 467s bits per cell: 16 467s cells: 1036.08M 467s hashes: 3 467s base min quality: 5 467s kmer min prob: 0.5 467s 467s target depth: 400 467s min depth: 3 467s max depth: 500 467s min good kmers: 15 467s depth percentile: 64.8 467s ignore dupe kmers: true 467s fix spikes: false 467s histogram length: 65536 467s print zero cov: false 467s 469s Made hash table: hashes = 3 mem = 1.93 GB cells = 1035.89M used = 0.000% 469s 469s Estimated unique kmers: 7 469s 469s Table creation time: 1.804 seconds. 469s Started output threads. 469s Started output threads. 469s Table read time: 0.014 seconds. 13.84 kb/sec 469s Total reads in: 2 0.000% Kept 469s Total bases in: 188 0.000% Kept 469s Error reads in: 2 100.000% 469s Error type 1: 2 100.000% 469s Error type 2: 0 0.000% 469s Error type 3: 0 0.000% 469s 469s Wrote histogram to hist.plt 469s Total kmers counted: 128 469s Total unique kmer count: 128 469s Includes forward kmers only. 469s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 469s The most accurate value is the greater of the two. 469s 469s Percent unique: 100.00% 469s Depth average: 1.00 (unique kmers) 469s Depth median: 1 (unique kmers) 469s Depth standard deviation: 0.00 (unique kmers) 469s Corrected depth average: 0.00 469s 469s Depth average: 1.00 (all kmers) 469s Depth median: 1 (all kmers) 469s Depth standard deviation: 0.00 (all kmers) 469s 469s Approx. read depth median: 1.47 469s 469s *********** Pass 2 ********** 469s 469s 469s Settings: 469s threads: 4 469s k: 31 469s deterministic: true 469s toss error reads: false 469s passes: 1 469s bits per cell: 16 469s cells: 1036.08M 469s hashes: 3 469s base min quality: 5 469s kmer min prob: 0.5 469s 469s target depth: 100 469s min depth: 5 469s max depth: 100 469s min good kmers: 15 469s depth percentile: 54.0 469s ignore dupe kmers: true 469s fix spikes: false 469s histogram length: 65536 469s 470s Made hash table: hashes = 3 mem = 1.93 GB cells = 1035.89M used = 0.000% 470s 470s Estimated unique kmers: 0 470s 470s Table creation time: 1.134 seconds. 470s Started output threads. 470s Started output threads. 470s Table read time: 0.003 seconds. 0.00 kb/sec 470s Total reads in: 0 NaN% Kept 470s Total bases in: 0 NaN% Kept 470s Error reads in: 0 NaN% 470s Error type 1: 0 NaN% 470s Error type 2: 0 NaN% 470s Error type 3: 0 NaN% 470s Total kmers counted: 0 470s Total unique kmer count: 0 470s Includes forward kmers only. 470s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 470s The most accurate value is the greater of the two. 470s 470s Percent unique: NaN% 470s Depth average: NaN (unique kmers) 470s Depth median: 0 (unique kmers) 470s Depth standard deviation: NaN (unique kmers) 470s Corrected depth average: NaN 470s 470s Depth average: NaN (all kmers) 470s Depth median: 0 (all kmers) 470s Depth standard deviation: 0.00 (all kmers) 470s 470s Approx. read depth median: NaN 470s 470s Removing temp files. 470s 470s Total time: 3.135 seconds. 0.06 kb/sec 470s test -r out3.fastq 470s test -r outt.fastq 470s test -r hist.plt 470s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 470s out=out4.fastq outt=outt2.fastq hist=hist2.plt 470s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 470s java -ea -Xmx2799m -Xms2799m -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 471s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 471s 471s 471s *********** Pass 1 ********** 471s 471s 471s Settings: 471s threads: 4 471s k: 31 471s deterministic: true 471s toss error reads: false 471s passes: 1 471s bits per cell: 16 471s cells: 1036.08M 471s hashes: 3 471s base min quality: 5 471s kmer min prob: 0.5 471s 471s target depth: 400 471s min depth: 3 471s max depth: 500 471s min good kmers: 15 471s depth percentile: 64.8 471s ignore dupe kmers: true 471s fix spikes: false 471s histogram length: 65536 471s print zero cov: false 471s 472s Made hash table: hashes = 3 mem = 1.93 GB cells = 1035.89M used = 0.000% 472s 472s Estimated unique kmers: 7 472s 472s Table creation time: 1.703 seconds. 472s Started output threads. 472s Started output threads. 472s Table read time: 0.010 seconds. 12.92 kb/sec 472s Total reads in: 2 0.000% Kept 472s Total bases in: 126 0.000% Kept 472s Error reads in: 2 100.000% 472s Error type 1: 2 100.000% 472s Error type 2: 0 0.000% 472s Error type 3: 0 0.000% 472s 472s Wrote histogram to hist2.plt 473s Total kmers counted: 66 473s Total unique kmer count: 66 473s Includes forward kmers only. 473s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 473s The most accurate value is the greater of the two. 473s 473s Percent unique: 100.00% 473s Depth average: 1.00 (unique kmers) 473s Depth median: 1 (unique kmers) 473s Depth standard deviation: 0.00 (unique kmers) 473s Corrected depth average: 0.00 473s 473s Depth average: 1.00 (all kmers) 473s Depth median: 1 (all kmers) 473s Depth standard deviation: 0.00 (all kmers) 473s 473s Approx. read depth median: 1.91 473s 473s *********** Pass 2 ********** 473s 473s 473s Settings: 473s threads: 4 473s k: 31 473s deterministic: true 473s toss error reads: false 473s passes: 1 473s bits per cell: 16 473s cells: 1036.08M 473s hashes: 3 473s base min quality: 5 473s kmer min prob: 0.5 473s 473s target depth: 100 473s min depth: 5 473s max depth: 100 473s min good kmers: 15 473s depth percentile: 54.0 473s ignore dupe kmers: true 473s fix spikes: false 473s histogram length: 65536 473s 474s Made hash table: hashes = 3 mem = 1.93 GB cells = 1035.89M used = 0.000% 474s 474s Estimated unique kmers: 0 474s 474s Table creation time: 1.102 seconds. 474s Started output threads. 474s Started output threads. 474s Table read time: 0.003 seconds. 0.00 kb/sec 474s Total reads in: 0 NaN% Kept 474s Total bases in: 0 NaN% Kept 474s Error reads in: 0 NaN% 474s Error type 1: 0 NaN% 474s Error type 2: 0 NaN% 474s Error type 3: 0 NaN% 474s Total kmers counted: 0 474s Total unique kmer count: 0 474s Includes forward kmers only. 474s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 474s The most accurate value is the greater of the two. 474s 474s Percent unique: NaN% 474s Depth average: NaN (unique kmers) 474s Depth median: 0 (unique kmers) 474s Depth standard deviation: NaN (unique kmers) 474s Corrected depth average: NaN 474s 474s Depth average: NaN (all kmers) 474s Depth median: 0 (all kmers) 474s Depth standard deviation: 0.00 (all kmers) 474s 474s Approx. read depth median: NaN 474s 474s Removing temp files. 474s 474s Total time: 2.984 seconds. 0.04 kb/sec 474s test -r out4.fastq 474s test -r outt2.fastq 474s test -r hist2.plt 474s autopkgtest [07:54:19]: test run-unit-test: -----------------------] 475s autopkgtest [07:54:20]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 475s run-unit-test PASS 475s autopkgtest [07:54:20]: @@@@@@@@@@@@@@@@@@@@ summary 475s run-unit-test PASS 498s Creating nova instance adt-noble-arm64-bbmap-20240321-074624-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240319.img (UUID bd25b89b-8264-4402-95d9-d9c88f21f275)...