0s autopkgtest [14:26:24]: starting date and time: 2025-03-15 14:26:24+0000 0s autopkgtest [14:26:24]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [14:26:24]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5izou6uv/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade porechop --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-20.secgroup --name adt-plucky-arm64-porechop-20250315-142624-juju-7f2275-prod-proposed-migration-environment-15-a182c5ca-4738-435f-925a-6192911a4c44 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 124s autopkgtest [14:28:28]: testbed dpkg architecture: arm64 124s autopkgtest [14:28:28]: testbed apt version: 2.9.33 124s autopkgtest [14:28:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup 124s autopkgtest [14:28:28]: testbed release detected to be: None 125s autopkgtest [14:28:29]: updating testbed package index (apt update) 126s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 126s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 126s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 126s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 126s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 126s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 127s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 127s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 127s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 127s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 127s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 130s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 130s + lsb_release --codename --short 130s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 130s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 130s Fetched 1094 kB in 2s (705 kB/s) 130s Reading package lists... 130s Reading package lists... 130s Building dependency tree...+ RELEASE=plucky 130s + cat 130s + [ plucky != trusty ] 130s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 130s 130s Reading state information... 130s Calculating upgrade... 131s Calculating upgrade... 131s The following packages will be upgraded: 131s python3-jinja2 strace 131s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s Need to get 608 kB of archives. 131s After this operation, 11.3 kB of additional disk space will be used. 131s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 132s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 132s Fetched 608 kB in 1s (709 kB/s) 133s (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 ... 117701 files and directories currently installed.) 133s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 133s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 133s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 133s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 133s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 133s Setting up strace (6.13+ds-1ubuntu1) ... 133s Processing triggers for man-db (2.13.0-1) ... 134s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 134s + /usr/lib/apt/apt-helper analyze-pattern ?true 134s + uname -r 134s + sed s/\./\\./g 134s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 134s + apt list ?obsolete 134s + tail -n+2 134s + grep -v ^linux-.*6\.14\.0-10-generic.* 134s + cut -d/ -f1 134s + obsolete_pkgs=linux-headers-6.11.0-8-generic 134s linux-headers-6.11.0-8 134s linux-image-6.11.0-8-generic 134s linux-modules-6.11.0-8-generic 134s linux-tools-6.11.0-8-generic 134s linux-tools-6.11.0-8 134s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 135s Solving dependencies... 135s The following packages will be REMOVED: 135s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 135s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 135s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 135s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 136s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 136s After this operation, 267 MB disk space will be freed. 136s (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 ... 117701 files and directories currently installed.) 136s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 136s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 136s Removing libpython3.12t64:arm64 (3.12.9-1) ... 136s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 136s Removing libnsl2:arm64 (1.3.0-3build3) ... 136s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 136s Removing libunwind8:arm64 (1.6.2-3.1) ... 136s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 136s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 138s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 138s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 138s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 138s /etc/kernel/postrm.d/initramfs-tools: 138s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 138s /etc/kernel/postrm.d/zz-flash-kernel: 138s flash-kernel: Kernel 6.11.0-8-generic has been removed. 138s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 138s /etc/kernel/postrm.d/zz-update-grub: 138s Sourcing file `/etc/default/grub' 138s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 138s Generating grub configuration file ... 138s Found linux image: /boot/vmlinuz-6.14.0-10-generic 138s Found initrd image: /boot/initrd.img-6.14.0-10-generic 139s Warning: os-prober will not be executed to detect other bootable partitions. 139s Systems on them will not be added to the GRUB boot configuration. 139s Check GRUB_DISABLE_OS_PROBER documentation entry. 139s Adding boot menu entry for UEFI Firmware Settings ... 139s done 139s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 139s Processing triggers for libc-bin (2.41-1ubuntu1) ... 139s (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 ... 81650 files and directories currently installed.) 139s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 139s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 139s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 139s + grep -q trusty /etc/lsb-release 139s + [ ! -d /usr/share/doc/unattended-upgrades ] 139s + [ ! -d /usr/share/doc/lxd ] 139s + [ ! -d /usr/share/doc/lxd-client ] 139s + [ ! -d /usr/share/doc/snapd ] 139s + type iptables 139s + cat 139s + chmod 755 /etc/rc.local 139s + . /etc/rc.local 139s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 139s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 139s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 139s + uname -m 139s + [ aarch64 = ppc64le ] 139s + [ -d /run/systemd/system ] 139s + systemd-detect-virt --quiet --vm 139s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 139s + cat 139s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 139s + echo COMPRESS=lz4 139s autopkgtest [14:28:43]: upgrading testbed (apt dist-upgrade and autopurge) 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 141s Starting 2 pkgProblemResolver with broken count: 0 141s Done 141s Entering ResolveByKeep 142s 142s Calculating upgrade... 142s The following packages will be upgraded: 142s libc-bin libc-dev-bin libc6 libc6-dev locales 142s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 142s Need to get 9530 kB of archives. 142s After this operation, 0 B of additional disk space will be used. 142s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 144s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 144s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 146s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 147s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 151s Preconfiguring packages ... 151s Fetched 9530 kB in 8s (1179 kB/s) 151s (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 ... 81647 files and directories currently installed.) 151s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 151s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 151s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 151s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 151s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 152s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 152s Setting up libc6:arm64 (2.41-1ubuntu2) ... 152s (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 ... 81647 files and directories currently installed.) 152s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 152s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 152s Setting up libc-bin (2.41-1ubuntu2) ... 152s (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 ... 81647 files and directories currently installed.) 152s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 152s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 152s Setting up locales (2.41-1ubuntu2) ... 153s Generating locales (this might take a while)... 155s en_US.UTF-8... done 155s Generation complete. 155s Setting up libc-dev-bin (2.41-1ubuntu2) ... 155s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 155s Processing triggers for man-db (2.13.0-1) ... 156s Processing triggers for systemd (257.3-1ubuntu3) ... 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s Starting pkgProblemResolver with broken count: 0 157s Starting 2 pkgProblemResolver with broken count: 0 157s Done 158s Solving dependencies... 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 159s autopkgtest [14:29:03]: rebooting testbed after setup commands that affected boot 182s autopkgtest [14:29:26]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 185s autopkgtest [14:29:29]: @@@@@@@@@@@@@@@@@@@@ apt-source porechop 187s Get:1 http://ftpmaster.internal/ubuntu plucky/universe porechop 0.2.4+dfsg-6 (dsc) [2215 B] 187s Get:2 http://ftpmaster.internal/ubuntu plucky/universe porechop 0.2.4+dfsg-6 (tar) [726 kB] 187s Get:3 http://ftpmaster.internal/ubuntu plucky/universe porechop 0.2.4+dfsg-6 (diff) [6152 B] 188s gpgv: Signature made Fri Jul 12 21:53:00 2024 UTC 188s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 188s gpgv: issuer "emollier@debian.org" 188s gpgv: Can't check signature: No public key 188s dpkg-source: warning: cannot verify inline signature for ./porechop_0.2.4+dfsg-6.dsc: no acceptable signature found 188s autopkgtest [14:29:32]: testing package porechop version 0.2.4+dfsg-6 189s autopkgtest [14:29:33]: build not needed 190s autopkgtest [14:29:34]: test run-unit-test: preparing testbed 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 191s Starting pkgProblemResolver with broken count: 0 191s Starting 2 pkgProblemResolver with broken count: 0 191s Done 191s The following NEW packages will be installed: 191s porechop 192s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 192s Need to get 56.5 kB of archives. 192s After this operation, 231 kB of additional disk space will be used. 192s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 porechop arm64 0.2.4+dfsg-6 [56.5 kB] 192s Fetched 56.5 kB in 0s (185 kB/s) 192s Selecting previously unselected package porechop. 192s (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 ... 81647 files and directories currently installed.) 192s Preparing to unpack .../porechop_0.2.4+dfsg-6_arm64.deb ... 192s Unpacking porechop (0.2.4+dfsg-6) ... 192s Setting up porechop (0.2.4+dfsg-6) ... 193s /usr/lib/python3/dist-packages/porechop/misc.py:261: SyntaxWarning: invalid escape sequence '\[' 193s row_str = re.sub('\033\[4m', '', row_str) 193s Processing triggers for man-db (2.13.0-1) ... 194s autopkgtest [14:29:38]: test run-unit-test: [----------------------- 195s usage: porechop -i INPUT [-o OUTPUT] 195s [--format {auto,fasta,fastq,fasta.gz,fastq.gz}] [-v VERBOSITY] 195s [-t THREADS] [-b BARCODE_DIR] 195s [--barcode_threshold BARCODE_THRESHOLD] 195s [--barcode_diff BARCODE_DIFF] [--require_two_barcodes] 195s [--untrimmed] [--discard_unassigned] 195s [--adapter_threshold ADAPTER_THRESHOLD] 195s [--check_reads CHECK_READS] [--scoring_scheme SCORING_SCHEME] 195s [--end_size END_SIZE] [--min_trim_size MIN_TRIM_SIZE] 195s [--extra_end_trim EXTRA_END_TRIM] 195s [--end_threshold END_THRESHOLD] [--no_split] 195s [--discard_middle] [--middle_threshold MIDDLE_THRESHOLD] 195s [--extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE] 195s [--extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE] 195s [--min_split_read_size MIN_SPLIT_READ_SIZE] [-h] [--version] 195s 195s Porechop: a tool for finding adapters in Oxford Nanopore reads, trimming them 195s from the ends and splitting reads with internal adapters 195s 195s Main options: 195s -i, --input INPUT FASTA/FASTQ of input reads or a directory which will 195s be recursively searched for FASTQ files (required) 195s -o, --output OUTPUT Filename for FASTA or FASTQ of trimmed reads (if not 195s set, trimmed reads will be printed to stdout) 195s --format {auto,fasta,fastq,fasta.gz,fastq.gz} 195s Output format for the reads - if auto, the format 195s will be chosen based on the output filename or the 195s input read format (default: auto) 195s -v, --verbosity VERBOSITY 195s Level of progress information: 0 = none, 1 = some, 2 195s = lots, 3 = full - output will go to stdout if reads 195s are saved to a file and stderr if reads are printed 195s to stdout (default: 1) 195s -t, --threads THREADS Number of threads to use for adapter alignment 195s (default: 2) 195s 195s Barcode binning settings: 195s Control the binning of reads based on barcodes (i.e. barcode 195s demultiplexing) 195s 195s -b, --barcode_dir BARCODE_DIR 195s Reads will be binned based on their barcode and 195s saved to separate files in this directory 195s (incompatible with --output) 195s --barcode_threshold BARCODE_THRESHOLD 195s A read must have at least this percent identity to a 195s barcode to be binned (default: 75.0) 195s --barcode_diff BARCODE_DIFF 195s If the difference between a read's best barcode 195s identity and its second-best barcode identity is 195s less than this value, it will not be put in a 195s barcode bin (to exclude cases which are too close to 195s call) (default: 5.0) 195s --require_two_barcodes Reads will only be put in barcode bins if they have 195s a strong match for the barcode on both their start 195s and end (default: a read can be binned with a match 195s at its start or end) 195s --untrimmed Bin reads but do not trim them (default: trim the 195s reads) 195s --discard_unassigned Discard unassigned reads (instead of creating a 195s "none" bin) (default: False) 195s 195s Adapter search settings: 195s Control how the program determines which adapter sets are present 195s 195s --adapter_threshold ADAPTER_THRESHOLD 195s An adapter set has to have at least this percent 195s identity to be labelled as present and trimmed off 195s (0 to 100) (default: 90.0) 195s --check_reads CHECK_READS 195s This many reads will be aligned to all possible 195s adapters to determine which adapter sets are present 195s (default: 10000) 195s --scoring_scheme SCORING_SCHEME 195s Comma-delimited string of alignment scores: match, 195s mismatch, gap open, gap extend (default: 3,-6,-5,-2) 195s 195s End adapter settings: 195s Control the trimming of adapters from read ends 195s 195s --end_size END_SIZE The number of base pairs at each end of the read 195s which will be searched for adapter sequences 195s (default: 150) 195s --min_trim_size MIN_TRIM_SIZE 195s Adapter alignments smaller than this will be ignored 195s (default: 4) 195s --extra_end_trim EXTRA_END_TRIM 195s This many additional bases will be removed next to 195s adapters found at the ends of reads (default: 2) 195s --end_threshold END_THRESHOLD 195s Adapters at the ends of reads must have at least 195s this percent identity to be removed (0 to 100) 195s (default: 75.0) 195s 195s Middle adapter settings: 195s Control the splitting of read from middle adapters 195s 195s --no_split Skip splitting reads based on middle adapters 195s (default: split reads when an adapter is found in 195s the middle) 195s --discard_middle Reads with middle adapters will be discarded 195s (default: reads with middle adapters are split) 195s (required for reads to be used with Nanopolish, this 195s option is on by default when outputting reads into 195s barcode bins) 195s --middle_threshold MIDDLE_THRESHOLD 195s Adapters in the middle of reads must have at least 195s this percent identity to be found (0 to 100) 195s (default: 90.0) 195s --extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE 195s This many additional bases will be removed next to 195s middle adapters on their "good" side (default: 10) 195s --extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE 195s This many additional bases will be removed next to 195s middle adapters on their "bad" side (default: 100) 195s --min_split_read_size MIN_SPLIT_READ_SIZE 195s Post-split read pieces smaller than this many base 195s pairs will not be outputted (default: 1000) 195s 195s Help: 195s -h, --help Show this help message and exit 195s --version Show program's version number and exit 195s autopkgtest [14:29:39]: test run-unit-test: -----------------------] 195s run-unit-test PASS (superficial) 195s autopkgtest [14:29:39]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 196s autopkgtest [14:29:40]: @@@@@@@@@@@@@@@@@@@@ summary 196s run-unit-test PASS (superficial) 214s nova [W] Using flock in prodstack6-arm64 214s Creating nova instance adt-plucky-arm64-porechop-20250315-142624-juju-7f2275-prod-proposed-migration-environment-15-a182c5ca-4738-435f-925a-6192911a4c44 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 214s nova [W] Timed out waiting for 8a2b1a99-e94e-4678-8f7a-90a0b372bb64 to get deleted.