0s autopkgtest [02:09:05]: starting date and time: 2024-07-13 02:09:05+0000 0s autopkgtest [02:09:05]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [02:09:05]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.t533tfc6/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/2.39-3.1ubuntu3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-s390x-4.secgroup --name adt-oracular-s390x-porechop-20240713-020904-juju-7f2275-prod-proposed-migration-environment-3-4d6a6d71-5379-46bd-84f0-77ce0f7a189b --image adt/ubuntu-oracular-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.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/ 85s autopkgtest [02:10:30]: testbed dpkg architecture: s390x 85s autopkgtest [02:10:30]: testbed apt version: 2.9.6 85s autopkgtest [02:10:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 86s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 86s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [48.2 kB] 86s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [3860 B] 86s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [366 kB] 86s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 86s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x Packages [93.1 kB] 86s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x c-n-f Metadata [2112 B] 86s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted s390x Packages [1368 B] 86s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted s390x c-n-f Metadata [120 B] 86s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x Packages [408 kB] 86s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x c-n-f Metadata [8372 B] 86s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse s390x Packages [2092 B] 86s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse s390x c-n-f Metadata [120 B] 87s Fetched 1068 kB in 1s (1343 kB/s) 87s Reading package lists... 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s Calculating upgrade... 90s The following packages will be upgraded: 90s binutils binutils-common binutils-s390x-linux-gnu gir1.2-glib-2.0 90s inetutils-telnet libbinutils libc-bin libc-dev-bin libc-devtools libc6 90s libc6-dev libctf-nobfd0 libctf0 libglib2.0-0t64 libglib2.0-data 90s libnghttp2-14 libnss3 libsframe1 libssl3t64 locales openssh-client 90s openssh-server openssh-sftp-server openssl telnet 90s 25 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s Need to get 20.4 MB of archives. 90s After this operation, 383 kB of additional disk space will be used. 90s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libc-devtools s390x 2.39-3.1ubuntu3 [30.7 kB] 90s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libc6-dev s390x 2.39-3.1ubuntu3 [1626 kB] 90s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libc-dev-bin s390x 2.39-3.1ubuntu3 [20.2 kB] 90s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libc6 s390x 2.39-3.1ubuntu3 [2841 kB] 90s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libc-bin s390x 2.39-3.1ubuntu3 [654 kB] 90s Get:6 http://ftpmaster.internal/ubuntu oracular/main s390x libssl3t64 s390x 3.2.2-1ubuntu1 [1837 kB] 91s Get:7 http://ftpmaster.internal/ubuntu oracular/main s390x openssh-sftp-server s390x 1:9.6p1-3ubuntu17 [38.2 kB] 91s Get:8 http://ftpmaster.internal/ubuntu oracular/main s390x openssh-server s390x 1:9.6p1-3ubuntu17 [525 kB] 91s Get:9 http://ftpmaster.internal/ubuntu oracular/main s390x openssh-client s390x 1:9.6p1-3ubuntu17 [928 kB] 91s Get:10 http://ftpmaster.internal/ubuntu oracular/main s390x gir1.2-glib-2.0 s390x 2.80.4-1ubuntu1 [180 kB] 91s Get:11 http://ftpmaster.internal/ubuntu oracular/main s390x libglib2.0-0t64 s390x 2.80.4-1ubuntu1 [1551 kB] 91s Get:12 http://ftpmaster.internal/ubuntu oracular/main s390x libglib2.0-data all 2.80.4-1ubuntu1 [49.3 kB] 91s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x locales all 2.39-3.1ubuntu3 [4220 kB] 91s Get:14 http://ftpmaster.internal/ubuntu oracular/main s390x openssl s390x 3.2.2-1ubuntu1 [1125 kB] 91s Get:15 http://ftpmaster.internal/ubuntu oracular/main s390x inetutils-telnet s390x 2:2.5-5ubuntu1 [110 kB] 91s Get:16 http://ftpmaster.internal/ubuntu oracular/main s390x libnghttp2-14 s390x 1.62.1-2 [76.9 kB] 91s Get:17 http://ftpmaster.internal/ubuntu oracular/main s390x telnet all 0.17+2.5-5ubuntu1 [3688 B] 91s Get:18 http://ftpmaster.internal/ubuntu oracular/main s390x libctf0 s390x 2.42.50.20240710-1ubuntu1 [100 kB] 91s Get:19 http://ftpmaster.internal/ubuntu oracular/main s390x libctf-nobfd0 s390x 2.42.50.20240710-1ubuntu1 [101 kB] 91s Get:20 http://ftpmaster.internal/ubuntu oracular/main s390x binutils-s390x-linux-gnu s390x 2.42.50.20240710-1ubuntu1 [2289 kB] 91s Get:21 http://ftpmaster.internal/ubuntu oracular/main s390x libbinutils s390x 2.42.50.20240710-1ubuntu1 [471 kB] 91s Get:22 http://ftpmaster.internal/ubuntu oracular/main s390x binutils s390x 2.42.50.20240710-1ubuntu1 [3062 B] 91s Get:23 http://ftpmaster.internal/ubuntu oracular/main s390x binutils-common s390x 2.42.50.20240710-1ubuntu1 [220 kB] 91s Get:24 http://ftpmaster.internal/ubuntu oracular/main s390x libsframe1 s390x 2.42.50.20240710-1ubuntu1 [13.8 kB] 91s Get:25 http://ftpmaster.internal/ubuntu oracular/main s390x libnss3 s390x 2:3.102-1 [1408 kB] 91s Preconfiguring packages ... 91s Fetched 20.4 MB in 1s (13.8 MB/s) 92s (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 ... 54721 files and directories currently installed.) 92s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu3_s390x.deb ... 92s Unpacking libc-devtools (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 92s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu3_s390x.deb ... 92s Unpacking libc6-dev:s390x (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 92s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu3_s390x.deb ... 92s Unpacking libc-dev-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 92s Preparing to unpack .../libc6_2.39-3.1ubuntu3_s390x.deb ... 92s Unpacking libc6:s390x (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 92s Setting up libc6:s390x (2.39-3.1ubuntu3) ... 92s Error: Could not restart systemd, systemd binary not working 92s (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 ... 54721 files and directories currently installed.) 92s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_s390x.deb ... 92s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 92s Setting up libc-bin (2.39-3.1ubuntu3) ... 92s (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 ... 54721 files and directories currently installed.) 92s Preparing to unpack .../libssl3t64_3.2.2-1ubuntu1_s390x.deb ... 92s Unpacking libssl3t64:s390x (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 92s Setting up libssl3t64:s390x (3.2.2-1ubuntu1) ... 92s (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 ... 54721 files and directories currently installed.) 92s Preparing to unpack .../00-openssh-sftp-server_1%3a9.6p1-3ubuntu17_s390x.deb ... 92s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 92s Preparing to unpack .../01-openssh-server_1%3a9.6p1-3ubuntu17_s390x.deb ... 93s Unpacking openssh-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 93s Preparing to unpack .../02-openssh-client_1%3a9.6p1-3ubuntu17_s390x.deb ... 93s Unpacking openssh-client (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 93s Preparing to unpack .../03-gir1.2-glib-2.0_2.80.4-1ubuntu1_s390x.deb ... 93s Unpacking gir1.2-glib-2.0:s390x (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 93s Preparing to unpack .../04-libglib2.0-0t64_2.80.4-1ubuntu1_s390x.deb ... 93s Unpacking libglib2.0-0t64:s390x (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 93s Preparing to unpack .../05-libglib2.0-data_2.80.4-1ubuntu1_all.deb ... 93s Unpacking libglib2.0-data (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 93s Preparing to unpack .../06-locales_2.39-3.1ubuntu3_all.deb ... 93s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 93s Preparing to unpack .../07-openssl_3.2.2-1ubuntu1_s390x.deb ... 93s Unpacking openssl (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 93s Preparing to unpack .../08-inetutils-telnet_2%3a2.5-5ubuntu1_s390x.deb ... 93s Unpacking inetutils-telnet (2:2.5-5ubuntu1) over (2:2.5-3ubuntu4) ... 93s Preparing to unpack .../09-libnghttp2-14_1.62.1-2_s390x.deb ... 93s Unpacking libnghttp2-14:s390x (1.62.1-2) over (1.62.1-1) ... 93s Preparing to unpack .../10-telnet_0.17+2.5-5ubuntu1_all.deb ... 93s Unpacking telnet (0.17+2.5-5ubuntu1) over (0.17+2.5-3ubuntu4) ... 93s Preparing to unpack .../11-libctf0_2.42.50.20240710-1ubuntu1_s390x.deb ... 93s Unpacking libctf0:s390x (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 93s Preparing to unpack .../12-libctf-nobfd0_2.42.50.20240710-1ubuntu1_s390x.deb ... 93s Unpacking libctf-nobfd0:s390x (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 93s Preparing to unpack .../13-binutils-s390x-linux-gnu_2.42.50.20240710-1ubuntu1_s390x.deb ... 93s Unpacking binutils-s390x-linux-gnu (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 93s Preparing to unpack .../14-libbinutils_2.42.50.20240710-1ubuntu1_s390x.deb ... 93s Unpacking libbinutils:s390x (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 93s Preparing to unpack .../15-binutils_2.42.50.20240710-1ubuntu1_s390x.deb ... 93s Unpacking binutils (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 93s Preparing to unpack .../16-binutils-common_2.42.50.20240710-1ubuntu1_s390x.deb ... 93s Unpacking binutils-common:s390x (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 93s Preparing to unpack .../17-libsframe1_2.42.50.20240710-1ubuntu1_s390x.deb ... 93s Unpacking libsframe1:s390x (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 93s Preparing to unpack .../18-libnss3_2%3a3.102-1_s390x.deb ... 93s Unpacking libnss3:s390x (2:3.102-1) over (2:3.101-1) ... 93s Setting up openssh-client (1:9.6p1-3ubuntu17) ... 93s Setting up binutils-common:s390x (2.42.50.20240710-1ubuntu1) ... 93s Setting up libnghttp2-14:s390x (1.62.1-2) ... 93s Setting up inetutils-telnet (2:2.5-5ubuntu1) ... 93s Setting up libctf-nobfd0:s390x (2.42.50.20240710-1ubuntu1) ... 93s Setting up libnss3:s390x (2:3.102-1) ... 93s Setting up locales (2.39-3.1ubuntu3) ... 94s Generating locales (this might take a while)... 96s en_US.UTF-8... done 96s Generation complete. 96s Setting up libsframe1:s390x (2.42.50.20240710-1ubuntu1) ... 96s Setting up libglib2.0-0t64:s390x (2.80.4-1ubuntu1) ... 96s No schema files found: doing nothing. 96s Setting up libglib2.0-data (2.80.4-1ubuntu1) ... 96s Setting up gir1.2-glib-2.0:s390x (2.80.4-1ubuntu1) ... 96s Setting up libbinutils:s390x (2.42.50.20240710-1ubuntu1) ... 96s Setting up libc-dev-bin (2.39-3.1ubuntu3) ... 96s Setting up openssl (3.2.2-1ubuntu1) ... 96s Installing new version of config file /etc/ssl/openssl.cnf ... 96s Setting up libc-devtools (2.39-3.1ubuntu3) ... 96s Setting up libctf0:s390x (2.42.50.20240710-1ubuntu1) ... 96s Setting up openssh-sftp-server (1:9.6p1-3ubuntu17) ... 96s Setting up binutils-s390x-linux-gnu (2.42.50.20240710-1ubuntu1) ... 96s Setting up telnet (0.17+2.5-5ubuntu1) ... 96s Setting up openssh-server (1:9.6p1-3ubuntu17) ... 96s Installing new version of config file /etc/pam.d/sshd ... 97s Setting up binutils (2.42.50.20240710-1ubuntu1) ... 97s Setting up libc6-dev:s390x (2.39-3.1ubuntu3) ... 97s Processing triggers for ufw (0.36.2-6) ... 97s Processing triggers for systemd (256-1ubuntu1) ... 98s Processing triggers for man-db (2.12.1-2) ... 99s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 100s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 100s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 100s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 101s Reading package lists... 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 102s Calculating upgrade... 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s autopkgtest [02:10:47]: rebooting testbed after setup commands that affected boot 106s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 130s autopkgtest [02:11:15]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:14:26 UTC 2024 132s autopkgtest [02:11:17]: @@@@@@@@@@@@@@@@@@@@ apt-source porechop 135s Get:1 http://ftpmaster.internal/ubuntu oracular/universe porechop 0.2.4+dfsg-4 (dsc) [2067 B] 135s Get:2 http://ftpmaster.internal/ubuntu oracular/universe porechop 0.2.4+dfsg-4 (tar) [726 kB] 135s Get:3 http://ftpmaster.internal/ubuntu oracular/universe porechop 0.2.4+dfsg-4 (diff) [6100 B] 135s gpgv: Signature made Tue Oct 18 09:07:13 2022 UTC 135s gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 135s gpgv: Can't check signature: No public key 135s dpkg-source: warning: cannot verify inline signature for ./porechop_0.2.4+dfsg-4.dsc: no acceptable signature found 135s autopkgtest [02:11:20]: testing package porechop version 0.2.4+dfsg-4 135s autopkgtest [02:11:20]: build not needed 136s autopkgtest [02:11:21]: test run-unit-test: preparing testbed 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s Starting pkgProblemResolver with broken count: 0 137s Starting 2 pkgProblemResolver with broken count: 0 137s Done 137s The following additional packages will be installed: 137s porechop 137s The following NEW packages will be installed: 137s autopkgtest-satdep porechop 137s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 137s Need to get 56.9 kB/57.6 kB of archives. 137s After this operation, 231 kB of additional disk space will be used. 137s Get:1 /tmp/autopkgtest.XPzbTu/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [704 B] 138s Get:2 http://ftpmaster.internal/ubuntu oracular/universe s390x porechop s390x 0.2.4+dfsg-4 [56.9 kB] 138s Fetched 56.9 kB in 0s (195 kB/s) 138s Selecting previously unselected package porechop. 138s (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 ... 54720 files and directories currently installed.) 138s Preparing to unpack .../porechop_0.2.4+dfsg-4_s390x.deb ... 138s Unpacking porechop (0.2.4+dfsg-4) ... 138s Selecting previously unselected package autopkgtest-satdep. 138s Preparing to unpack .../1-autopkgtest-satdep.deb ... 138s Unpacking autopkgtest-satdep (0) ... 138s Setting up porechop (0.2.4+dfsg-4) ... 138s /usr/lib/python3/dist-packages/porechop/misc.py:261: SyntaxWarning: invalid escape sequence '\[' 138s row_str = re.sub('\033\[4m', '', row_str) 138s Setting up autopkgtest-satdep (0) ... 138s Processing triggers for man-db (2.12.1-2) ... 141s (Reading database ... 54740 files and directories currently installed.) 141s Removing autopkgtest-satdep (0) ... 141s autopkgtest [02:11:26]: test run-unit-test: [----------------------- 142s usage: porechop -i INPUT [-o OUTPUT] 142s [--format {auto,fasta,fastq,fasta.gz,fastq.gz}] [-v VERBOSITY] 142s [-t THREADS] [-b BARCODE_DIR] 142s [--barcode_threshold BARCODE_THRESHOLD] 142s [--barcode_diff BARCODE_DIFF] [--require_two_barcodes] 142s [--untrimmed] [--discard_unassigned] 142s [--adapter_threshold ADAPTER_THRESHOLD] 142s [--check_reads CHECK_READS] [--scoring_scheme SCORING_SCHEME] 142s [--end_size END_SIZE] [--min_trim_size MIN_TRIM_SIZE] 142s [--extra_end_trim EXTRA_END_TRIM] 142s [--end_threshold END_THRESHOLD] [--no_split] 142s [--discard_middle] [--middle_threshold MIDDLE_THRESHOLD] 142s [--extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE] 142s [--extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE] 142s [--min_split_read_size MIN_SPLIT_READ_SIZE] [-h] [--version] 142s 142s Porechop: a tool for finding adapters in Oxford Nanopore reads, trimming them 142s from the ends and splitting reads with internal adapters 142s 142s Main options: 142s -i INPUT, --input INPUT 142s FASTA/FASTQ of input reads or a directory which will 142s be recursively searched for FASTQ files (required) 142s -o OUTPUT, --output OUTPUT 142s Filename for FASTA or FASTQ of trimmed reads (if not 142s set, trimmed reads will be printed to stdout) 142s --format {auto,fasta,fastq,fasta.gz,fastq.gz} 142s Output format for the reads - if auto, the format 142s will be chosen based on the output filename or the 142s input read format (default: auto) 142s -v VERBOSITY, --verbosity VERBOSITY 142s Level of progress information: 0 = none, 1 = some, 2 142s = lots, 3 = full - output will go to stdout if reads 142s are saved to a file and stderr if reads are printed 142s to stdout (default: 1) 142s -t THREADS, --threads THREADS 142s Number of threads to use for adapter alignment 142s (default: 1) 142s 142s Barcode binning settings: 142s Control the binning of reads based on barcodes (i.e. barcode 142s demultiplexing) 142s 142s -b BARCODE_DIR, --barcode_dir BARCODE_DIR 142s Reads will be binned based on their barcode and 142s saved to separate files in this directory 142s (incompatible with --output) 142s --barcode_threshold BARCODE_THRESHOLD 142s A read must have at least this percent identity to a 142s barcode to be binned (default: 75.0) 142s --barcode_diff BARCODE_DIFF 142s If the difference between a read's best barcode 142s identity and its second-best barcode identity is 142s less than this value, it will not be put in a 142s barcode bin (to exclude cases which are too close to 142s call) (default: 5.0) 142s --require_two_barcodes Reads will only be put in barcode bins if they have 142s a strong match for the barcode on both their start 142s and end (default: a read can be binned with a match 142s at its start or end) 142s --untrimmed Bin reads but do not trim them (default: trim the 142s reads) 142s --discard_unassigned Discard unassigned reads (instead of creating a 142s "none" bin) (default: False) 142s 142s Adapter search settings: 142s Control how the program determines which adapter sets are present 142s 142s --adapter_threshold ADAPTER_THRESHOLD 142s An adapter set has to have at least this percent 142s identity to be labelled as present and trimmed off 142s (0 to 100) (default: 90.0) 142s --check_reads CHECK_READS 142s This many reads will be aligned to all possible 142s adapters to determine which adapter sets are present 142s (default: 10000) 142s --scoring_scheme SCORING_SCHEME 142s Comma-delimited string of alignment scores: match, 142s mismatch, gap open, gap extend (default: 3,-6,-5,-2) 142s 142s End adapter settings: 142s Control the trimming of adapters from read ends 142s 142s --end_size END_SIZE The number of base pairs at each end of the read 142s which will be searched for adapter sequences 142s (default: 150) 142s --min_trim_size MIN_TRIM_SIZE 142s Adapter alignments smaller than this will be ignored 142s (default: 4) 142s --extra_end_trim EXTRA_END_TRIM 142s This many additional bases will be removed next to 142s adapters found at the ends of reads (default: 2) 142s --end_threshold END_THRESHOLD 142s Adapters at the ends of reads must have at least 142s this percent identity to be removed (0 to 100) 142s (default: 75.0) 142s 142s Middle adapter settings: 142s Control the splitting of read from middle adapters 142s 142s --no_split Skip splitting reads based on middle adapters 142s (default: split reads when an adapter is found in 142s the middle) 142s --discard_middle Reads with middle adapters will be discarded 142s (default: reads with middle adapters are split) 142s (required for reads to be used with Nanopolish, this 142s option is on by default when outputting reads into 142s barcode bins) 142s --middle_threshold MIDDLE_THRESHOLD 142s Adapters in the middle of reads must have at least 142s this percent identity to be found (0 to 100) 142s (default: 90.0) 142s --extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE 142s This many additional bases will be removed next to 142s middle adapters on their "good" side (default: 10) 142s --extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE 142s This many additional bases will be removed next to 142s middle adapters on their "bad" side (default: 100) 142s --min_split_read_size MIN_SPLIT_READ_SIZE 142s Post-split read pieces smaller than this many base 142s pairs will not be outputted (default: 1000) 142s 142s Help: 142s -h, --help Show this help message and exit 142s --version Show program's version number and exit 142s autopkgtest [02:11:27]: test run-unit-test: -----------------------] 142s run-unit-test PASS (superficial) 142s autopkgtest [02:11:27]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 143s autopkgtest [02:11:28]: @@@@@@@@@@@@@@@@@@@@ summary 143s run-unit-test PASS (superficial) 155s nova [W] Using flock in scalingstack-bos01-s390x 155s Creating nova instance adt-oracular-s390x-porechop-20240713-020904-juju-7f2275-prod-proposed-migration-environment-3-4d6a6d71-5379-46bd-84f0-77ce0f7a189b from image adt/ubuntu-oracular-s390x-server-20240711.img (UUID cd7d8501-1120-4d80-87a5-5946a33c5d4a)...