0s autopkgtest [15:20:34]: starting date and time: 2025-03-15 15:20:34+0000 0s autopkgtest [15:20:34]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:20:34]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pe51f_ed/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.149 lxd-armhf-10.145.243.149:autopkgtest/ubuntu/plucky/armhf 23s autopkgtest [15:20:57]: testbed dpkg architecture: armhf 25s autopkgtest [15:20:59]: testbed apt version: 2.9.33 30s autopkgtest [15:21:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup 32s autopkgtest [15:21:06]: testbed release detected to be: None 40s autopkgtest [15:21:14]: updating testbed package index (apt update) 43s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 43s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 43s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 43s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 43s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 43s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 43s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 43s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [81.0 kB] 43s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1944 B] 43s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 43s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [326 kB] 43s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [12.1 kB] 43s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 43s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [332 B] 43s Get:15 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 45s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1400 kB] 45s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 45s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 45s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 45s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 45s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 46s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 49s Fetched 41.0 MB in 6s (6681 kB/s) 50s Reading package lists... 57s autopkgtest [15:21:31]: upgrading testbed (apt dist-upgrade and autopurge) 58s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 59s Starting 2 pkgProblemResolver with broken count: 0 59s Done 60s Entering ResolveByKeep 60s 60s Calculating upgrade... 61s The following packages will be upgraded: 61s libc-bin libc6 locales python3-jinja2 sos strace 61s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s Need to get 8642 kB of archives. 61s After this operation, 23.6 kB of additional disk space will be used. 61s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 62s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 62s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 62s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 62s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 62s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 62s Preconfiguring packages ... 63s Fetched 8642 kB in 1s (8049 kB/s) 63s (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 ... 64655 files and directories currently installed.) 63s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 63s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 63s Setting up libc6:armhf (2.41-1ubuntu2) ... 63s (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 ... 64655 files and directories currently installed.) 63s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 63s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 63s Setting up libc-bin (2.41-1ubuntu2) ... 64s (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 ... 64655 files and directories currently installed.) 64s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 64s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 64s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 64s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 64s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 64s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 64s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 64s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 64s Setting up sos (4.9.0-5) ... 65s Setting up locales (2.41-1ubuntu2) ... 66s Generating locales (this might take a while)... 68s en_US.UTF-8... done 68s Generation complete. 68s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 68s Setting up strace (6.13+ds-1ubuntu1) ... 68s Processing triggers for man-db (2.13.0-1) ... 69s Processing triggers for systemd (257.3-1ubuntu3) ... 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 72s Starting pkgProblemResolver with broken count: 0 73s Starting 2 pkgProblemResolver with broken count: 0 73s Done 73s Solving dependencies... 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s autopkgtest [15:21:49]: rebooting testbed after setup commands that affected boot 123s autopkgtest [15:22:37]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 159s autopkgtest [15:23:13]: @@@@@@@@@@@@@@@@@@@@ apt-source porechop 170s Get:1 http://ftpmaster.internal/ubuntu plucky/universe porechop 0.2.4+dfsg-6 (dsc) [2215 B] 170s Get:2 http://ftpmaster.internal/ubuntu plucky/universe porechop 0.2.4+dfsg-6 (tar) [726 kB] 170s Get:3 http://ftpmaster.internal/ubuntu plucky/universe porechop 0.2.4+dfsg-6 (diff) [6152 B] 170s gpgv: Signature made Fri Jul 12 21:53:00 2024 UTC 170s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 170s gpgv: issuer "emollier@debian.org" 170s gpgv: Can't check signature: No public key 170s dpkg-source: warning: cannot verify inline signature for ./porechop_0.2.4+dfsg-6.dsc: no acceptable signature found 170s autopkgtest [15:23:24]: testing package porechop version 0.2.4+dfsg-6 172s autopkgtest [15:23:26]: build not needed 174s autopkgtest [15:23:28]: test run-unit-test: preparing testbed 176s Reading package lists... 177s Building dependency tree... 177s Reading state information... 177s Starting pkgProblemResolver with broken count: 0 177s Starting 2 pkgProblemResolver with broken count: 0 177s Done 178s The following NEW packages will be installed: 178s porechop 178s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 178s Need to get 55.6 kB of archives. 178s After this operation, 210 kB of additional disk space will be used. 178s Get:1 http://ftpmaster.internal/ubuntu plucky/universe armhf porechop armhf 0.2.4+dfsg-6 [55.6 kB] 179s Fetched 55.6 kB in 0s (180 kB/s) 179s Selecting previously unselected package porechop. 179s (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 ... 64655 files and directories currently installed.) 179s Preparing to unpack .../porechop_0.2.4+dfsg-6_armhf.deb ... 179s Unpacking porechop (0.2.4+dfsg-6) ... 179s Setting up porechop (0.2.4+dfsg-6) ... 179s /usr/lib/python3/dist-packages/porechop/misc.py:261: SyntaxWarning: invalid escape sequence '\[' 179s row_str = re.sub('\033\[4m', '', row_str) 179s Processing triggers for man-db (2.13.0-1) ... 187s autopkgtest [15:23:41]: test run-unit-test: [----------------------- 189s usage: porechop -i INPUT [-o OUTPUT] 189s [--format {auto,fasta,fastq,fasta.gz,fastq.gz}] [-v VERBOSITY] 189s [-t THREADS] [-b BARCODE_DIR] 189s [--barcode_threshold BARCODE_THRESHOLD] 189s [--barcode_diff BARCODE_DIFF] [--require_two_barcodes] 189s [--untrimmed] [--discard_unassigned] 189s [--adapter_threshold ADAPTER_THRESHOLD] 189s [--check_reads CHECK_READS] [--scoring_scheme SCORING_SCHEME] 189s [--end_size END_SIZE] [--min_trim_size MIN_TRIM_SIZE] 189s [--extra_end_trim EXTRA_END_TRIM] 189s [--end_threshold END_THRESHOLD] [--no_split] 189s [--discard_middle] [--middle_threshold MIDDLE_THRESHOLD] 189s [--extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE] 189s [--extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE] 189s [--min_split_read_size MIN_SPLIT_READ_SIZE] [-h] [--version] 189s 189s Porechop: a tool for finding adapters in Oxford Nanopore reads, trimming them 189s from the ends and splitting reads with internal adapters 189s 189s Main options: 189s -i, --input INPUT FASTA/FASTQ of input reads or a directory which will 189s be recursively searched for FASTQ files (required) 189s -o, --output OUTPUT Filename for FASTA or FASTQ of trimmed reads (if not 189s set, trimmed reads will be printed to stdout) 189s --format {auto,fasta,fastq,fasta.gz,fastq.gz} 189s Output format for the reads - if auto, the format 189s will be chosen based on the output filename or the 189s input read format (default: auto) 189s -v, --verbosity VERBOSITY 189s Level of progress information: 0 = none, 1 = some, 2 189s = lots, 3 = full - output will go to stdout if reads 189s are saved to a file and stderr if reads are printed 189s to stdout (default: 1) 189s -t, --threads THREADS Number of threads to use for adapter alignment 189s (default: 8) 189s 189s Barcode binning settings: 189s Control the binning of reads based on barcodes (i.e. barcode 189s demultiplexing) 189s 189s -b, --barcode_dir BARCODE_DIR 189s Reads will be binned based on their barcode and 189s saved to separate files in this directory 189s (incompatible with --output) 189s --barcode_threshold BARCODE_THRESHOLD 189s A read must have at least this percent identity to a 189s barcode to be binned (default: 75.0) 189s --barcode_diff BARCODE_DIFF 189s If the difference between a read's best barcode 189s identity and its second-best barcode identity is 189s less than this value, it will not be put in a 189s barcode bin (to exclude cases which are too close to 189s call) (default: 5.0) 189s --require_two_barcodes Reads will only be put in barcode bins if they have 189s a strong match for the barcode on both their start 189s and end (default: a read can be binned with a match 189s at its start or end) 189s --untrimmed Bin reads but do not trim them (default: trim the 189s reads) 189s --discard_unassigned Discard unassigned reads (instead of creating a 189s "none" bin) (default: False) 189s 189s Adapter search settings: 189s Control how the program determines which adapter sets are present 189s 189s --adapter_threshold ADAPTER_THRESHOLD 189s An adapter set has to have at least this percent 189s identity to be labelled as present and trimmed off 189s (0 to 100) (default: 90.0) 189s --check_reads CHECK_READS 189s This many reads will be aligned to all possible 189s adapters to determine which adapter sets are present 189s (default: 10000) 189s --scoring_scheme SCORING_SCHEME 189s Comma-delimited string of alignment scores: match, 189s mismatch, gap open, gap extend (default: 3,-6,-5,-2) 189s 189s End adapter settings: 189s Control the trimming of adapters from read ends 189s 189s --end_size END_SIZE The number of base pairs at each end of the read 189s which will be searched for adapter sequences 189s (default: 150) 189s --min_trim_size MIN_TRIM_SIZE 189s Adapter alignments smaller than this will be ignored 189s (default: 4) 189s --extra_end_trim EXTRA_END_TRIM 189s This many additional bases will be removed next to 189s adapters found at the ends of reads (default: 2) 189s --end_threshold END_THRESHOLD 189s Adapters at the ends of reads must have at least 189s this percent identity to be removed (0 to 100) 189s (default: 75.0) 189s 189s Middle adapter settings: 189s Control the splitting of read from middle adapters 189s 189s --no_split Skip splitting reads based on middle adapters 189s (default: split reads when an adapter is found in 189s the middle) 189s --discard_middle Reads with middle adapters will be discarded 189s (default: reads with middle adapters are split) 189s (required for reads to be used with Nanopolish, this 189s option is on by default when outputting reads into 189s barcode bins) 189s --middle_threshold MIDDLE_THRESHOLD 189s Adapters in the middle of reads must have at least 189s this percent identity to be found (0 to 100) 189s (default: 90.0) 189s --extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE 189s This many additional bases will be removed next to 189s middle adapters on their "good" side (default: 10) 189s --extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE 189s This many additional bases will be removed next to 189s middle adapters on their "bad" side (default: 100) 189s --min_split_read_size MIN_SPLIT_READ_SIZE 189s Post-split read pieces smaller than this many base 189s pairs will not be outputted (default: 1000) 189s 189s Help: 189s -h, --help Show this help message and exit 189s --version Show program's version number and exit 190s autopkgtest [15:23:44]: test run-unit-test: -----------------------] 194s run-unit-test PASS (superficial) 194s autopkgtest [15:23:48]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 198s autopkgtest [15:23:52]: @@@@@@@@@@@@@@@@@@@@ summary 198s run-unit-test PASS (superficial)