0s autopkgtest [15:32:18]: starting date and time: 2025-03-15 15:32:18+0000 0s autopkgtest [15:32:18]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:32:18]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yutfrry7/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 pyfastx --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.188 lxd-armhf-10.145.243.188:autopkgtest/ubuntu/plucky/armhf 28s autopkgtest [15:32:46]: testbed dpkg architecture: armhf 30s autopkgtest [15:32:48]: testbed apt version: 2.9.33 33s autopkgtest [15:32:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup 35s autopkgtest [15:32:53]: testbed release detected to be: None 43s autopkgtest [15:33:01]: updating testbed package index (apt update) 46s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 46s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 46s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 47s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 47s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 47s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 47s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 47s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [81.0 kB] 47s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1944 B] 47s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 47s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [326 kB] 48s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [12.1 kB] 48s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 48s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [332 B] 48s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 48s Get:16 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 72s Get:17 http://ftpmaster.internal/ubuntu plucky/main Sources [1400 kB] 73s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 75s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 75s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 75s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 91s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 93s Fetched 41.0 MB in 47s (864 kB/s) 94s Reading package lists... 100s autopkgtest [15:33:58]: upgrading testbed (apt dist-upgrade and autopurge) 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 103s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 104s Starting 2 pkgProblemResolver with broken count: 0 104s Done 105s Entering ResolveByKeep 105s 106s Calculating upgrade... 106s The following packages will be upgraded: 106s libc-bin libc6 locales python3-jinja2 sos strace 107s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Need to get 8642 kB of archives. 107s After this operation, 23.6 kB of additional disk space will be used. 107s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 110s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 111s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 116s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 116s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 117s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 117s Preconfiguring packages ... 118s Fetched 8642 kB in 11s (820 kB/s) 118s (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.) 118s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 118s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 118s Setting up libc6:armhf (2.41-1ubuntu2) ... 118s (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.) 118s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 118s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 118s Setting up libc-bin (2.41-1ubuntu2) ... 119s (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.) 119s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 119s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 119s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 119s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 119s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 119s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 119s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 120s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 120s Setting up sos (4.9.0-5) ... 121s Setting up locales (2.41-1ubuntu2) ... 122s Generating locales (this might take a while)... 124s en_US.UTF-8... done 124s Generation complete. 124s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 125s Setting up strace (6.13+ds-1ubuntu1) ... 125s Processing triggers for man-db (2.13.0-1) ... 126s Processing triggers for systemd (257.3-1ubuntu3) ... 128s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s Starting pkgProblemResolver with broken count: 0 130s Starting 2 pkgProblemResolver with broken count: 0 130s Done 130s Solving dependencies... 131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s autopkgtest [15:34:31]: rebooting testbed after setup commands that affected boot 173s autopkgtest [15:35:11]: 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 197s autopkgtest [15:35:35]: @@@@@@@@@@@@@@@@@@@@ apt-source pyfastx 211s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.2.0-1build1 (dsc) [2171 B] 211s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.2.0-1build1 (tar) [231 kB] 211s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.2.0-1build1 (diff) [7896 B] 211s gpgv: Signature made Tue Mar 4 15:58:37 2025 UTC 211s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 211s gpgv: Can't check signature: No public key 211s dpkg-source: warning: cannot verify inline signature for ./pyfastx_2.2.0-1build1.dsc: no acceptable signature found 211s autopkgtest [15:35:49]: testing package pyfastx version 2.2.0-1build1 213s autopkgtest [15:35:51]: build not needed 215s autopkgtest [15:35:53]: test run-unit-test: preparing testbed 217s Reading package lists... 218s Building dependency tree... 218s Reading state information... 218s Starting pkgProblemResolver with broken count: 0 219s Starting 2 pkgProblemResolver with broken count: 0 219s Done 220s The following NEW packages will be installed: 220s pyfastx python3-all python3-importlib-metadata python3-pyfaidx 220s python3-pyfastx 220s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 220s Need to get 226 kB of archives. 220s After this operation, 580 kB of additional disk space will be used. 220s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf python3-importlib-metadata all 8.6.1-1 [20.7 kB] 220s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 220s Get:3 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pyfastx armhf 2.2.0-1build1 [53.0 kB] 221s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf pyfastx armhf 2.2.0-1build1 [122 kB] 221s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.13.2-2 [886 B] 221s Fetched 226 kB in 1s (406 kB/s) 221s Selecting previously unselected package python3-importlib-metadata. 221s (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.) 221s Preparing to unpack .../python3-importlib-metadata_8.6.1-1_all.deb ... 221s Unpacking python3-importlib-metadata (8.6.1-1) ... 221s Selecting previously unselected package python3-pyfaidx. 221s Preparing to unpack .../python3-pyfaidx_0.8.1.3-1_all.deb ... 221s Unpacking python3-pyfaidx (0.8.1.3-1) ... 221s Selecting previously unselected package python3-pyfastx. 221s Preparing to unpack .../python3-pyfastx_2.2.0-1build1_armhf.deb ... 221s Unpacking python3-pyfastx (2.2.0-1build1) ... 221s Selecting previously unselected package pyfastx. 222s Preparing to unpack .../pyfastx_2.2.0-1build1_armhf.deb ... 222s Unpacking pyfastx (2.2.0-1build1) ... 222s Selecting previously unselected package python3-all. 222s Preparing to unpack .../python3-all_3.13.2-2_armhf.deb ... 222s Unpacking python3-all (3.13.2-2) ... 222s Setting up python3-importlib-metadata (8.6.1-1) ... 222s Setting up python3-all (3.13.2-2) ... 222s Setting up python3-pyfaidx (0.8.1.3-1) ... 222s Setting up python3-pyfastx (2.2.0-1build1) ... 222s Setting up pyfastx (2.2.0-1build1) ... 222s Processing triggers for man-db (2.13.0-1) ... 232s autopkgtest [15:36:10]: test run-unit-test: [----------------------- 234s test_id_exception (tests.test_fakeys.IdentifierTest.test_id_exception) ... ok 235s test_key_identifier (tests.test_fakeys.IdentifierTest.test_key_identifier) ... ok 235s test_key_repr (tests.test_fakeys.IdentifierTest.test_key_repr) ... ok 235s test_key_slice (tests.test_fakeys.IdentifierTest.test_key_slice) ... ok 235s test_keys_filter (tests.test_fakeys.IdentifierTest.test_keys_filter) ... ok 235s test_keys_sort (tests.test_fakeys.IdentifierTest.test_keys_sort) ... ok 235s test_build (tests.test_fasta.FastaTest.test_build) ... ok 235s test_exception (tests.test_fasta.FastaTest.test_exception) ... ok 235s test_fasta (tests.test_fasta.FastaTest.test_fasta) ... ok 235s test_iter_full_name (tests.test_fasta.FastaTest.test_iter_full_name) ... ok 235s test_iter_object (tests.test_fasta.FastaTest.test_iter_object) ... ok 235s test_iter_tuple (tests.test_fasta.FastaTest.test_iter_tuple) ... ok 235s test_iter_upper (tests.test_fasta.FastaTest.test_iter_upper) ... ok 236s test_iter_upper_full_name (tests.test_fasta.FastaTest.test_iter_upper_full_name) ... ok 236s test_key_func (tests.test_fasta.FastaTest.test_key_func) ... ok 236s test_module (tests.test_fasta.FastaTest.test_module) ... ok 236s test_no_upper (tests.test_fasta.FastaTest.test_no_upper) ... ok 236s test_repr (tests.test_fasta.FastaTest.test_repr) ... ok 236s test_seq_fetch (tests.test_fasta.FastaTest.test_seq_fetch) ... ok 236s test_seq_flank (tests.test_fasta.FastaTest.test_seq_flank) ... ok 236s test_seq_type (tests.test_fasta.FastaTest.test_seq_type) ... ok 236s test_statistics (tests.test_fasta.FastaTest.test_statistics) ... ok 237s test_build (tests.test_fastq.FastqTest.test_build) ... ok 237s test_exception (tests.test_fastq.FastqTest.test_exception) ... ok 237s test_fastq (tests.test_fastq.FastqTest.test_fastq) ... ok 237s test_full_name (tests.test_fastq.FastqTest.test_full_name) ... ok 237s test_iter_object (tests.test_fastq.FastqTest.test_iter_object) ... ok 237s test_iter_tuple (tests.test_fastq.FastqTest.test_iter_tuple) ... ok 238s test_negative (tests.test_fastq.FastqTest.test_negative) ... ok 238s test_platform (tests.test_fastq.FastqTest.test_platform) ... ok 238s test_read_len (tests.test_fastq.FastqTest.test_read_len) ... ok 238s test_repr (tests.test_fastq.FastqTest.test_repr) ... ok 238s test_exception (tests.test_fastx.FastxTest.test_exception) ... ok 238s test_fasta_iter (tests.test_fastx.FastxTest.test_fasta_iter) ... ok 238s test_fasta_upper (tests.test_fastx.FastxTest.test_fasta_upper) ... ok 238s test_fastq_iter (tests.test_fastx.FastxTest.test_fastq_iter) ... ok 238s test_fastx_repr (tests.test_fastx.FastxTest.test_fastx_repr) ... ok 238s test_exception (tests.test_fqkeys.FastxTest.test_exception) ... ok 238s test_fastq_key (tests.test_fqkeys.FastxTest.test_fastq_key) ... ok 238s test_read (tests.test_read.ReadTest.test_read) ... ok 238s test_read_description (tests.test_read.ReadTest.test_read_description) ... ok 238s test_read_raw (tests.test_read.ReadTest.test_read_raw) ... ok 239s test_read_seq (tests.test_read.ReadTest.test_read_seq) ... ok 239s test_repr (tests.test_read.ReadTest.test_repr) ... ok 239s test_full_compo (tests.test_sequence.SequenceTest.test_full_compo) ... ok 239s test_seq_by_index (tests.test_sequence.SequenceTest.test_seq_by_index) ... ok 239s test_seq_by_key (tests.test_sequence.SequenceTest.test_seq_by_key) ... ok 239s test_seq_content (tests.test_sequence.SequenceTest.test_seq_content) ... ok 239s test_seq_exception (tests.test_sequence.SequenceTest.test_seq_exception) ... ok 239s test_seq_iter (tests.test_sequence.SequenceTest.test_seq_iter) ... ok 239s test_seq_raw (tests.test_sequence.SequenceTest.test_seq_raw) ... ok 239s test_seq_repr (tests.test_sequence.SequenceTest.test_seq_repr) ... ok 239s test_seq_reverse_complement (tests.test_sequence.SequenceTest.test_seq_reverse_complement) ... ok 239s test_seq_slice (tests.test_sequence.SequenceTest.test_seq_slice) ... ok 239s test_seq_by_index (tests.test_sequence_error.SequenceErrorTest.test_seq_by_index) ... ok 239s test_seq_by_key (tests.test_sequence_error.SequenceErrorTest.test_seq_by_key) ... ok 239s 239s ---------------------------------------------------------------------- 239s Ran 56 tests in 5.102s 239s 239s OK 240s autopkgtest [15:36:18]: test run-unit-test: -----------------------] 244s autopkgtest [15:36:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 244s run-unit-test PASS 248s autopkgtest [15:36:26]: test test-cli: preparing testbed 270s autopkgtest [15:36:48]: testbed dpkg architecture: armhf 272s autopkgtest [15:36:50]: testbed apt version: 2.9.33 276s autopkgtest [15:36:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 278s autopkgtest [15:36:56]: testbed release detected to be: plucky 285s autopkgtest [15:37:03]: updating testbed package index (apt update) 287s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 287s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 288s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 288s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 288s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 288s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 288s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 289s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 289s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 289s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 289s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 290s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 290s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 290s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 290s Get:15 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 292s Get:16 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 330s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 330s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 333s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 333s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 333s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 351s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 353s Fetched 41.0 MB in 1min 6s (626 kB/s) 354s Reading package lists... 359s autopkgtest [15:38:17]: upgrading testbed (apt dist-upgrade and autopurge) 361s Reading package lists... 361s Building dependency tree... 361s Reading state information... 362s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 362s Starting 2 pkgProblemResolver with broken count: 0 362s Done 363s Entering ResolveByKeep 363s 363s Calculating upgrade... 364s The following packages will be upgraded: 364s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 364s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 364s Need to get 8683 kB of archives. 364s After this operation, 23.6 kB of additional disk space will be used. 364s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 368s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 368s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 373s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 373s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 373s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 374s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 375s Preconfiguring packages ... 375s Fetched 8683 kB in 11s (820 kB/s) 375s (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.) 375s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 375s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 376s Setting up libc6:armhf (2.41-1ubuntu2) ... 376s (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.) 376s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 376s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 376s Setting up libc-bin (2.41-1ubuntu2) ... 376s (Reading database ... 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Found pyfastx commands: 'index stat split fq2fa subseq sample extract' 477s $ pyfastx index --help 477s usage: pyfastx index [-h] [-f] fastx [fastx ...] 477s 477s positional arguments: 477s fastx fasta or fastq file, gzip support 477s 477s options: 477s -h, --help show this help message and exit 477s -f, --full build full index, base composition will be calculated 477s $ pyfastx stat --help 478s usage: pyfastx stat [-h] fastx [fastx ...] 478s 478s positional arguments: 478s fastx fasta or fastq file, gzip support 478s 478s options: 478s -h, --help show this help message and exit 478s $ pyfastx split --help 478s usage: pyfastx split [-h] (-n int | -c int) [-o str] fastx 478s 478s positional arguments: 478s fastx fasta or fastq file, gzip support 478s 478s options: 478s -h, --help show this help message and exit 478s -n int split a fasta/q file into N new files with even size 478s -c int split a fasta/q file into multiple files containing the 478s same sequence counts 478s -o, --out-dir str output directory, default is current folder 478s $ pyfastx fq2fa --help 478s usage: pyfastx fq2fa [-h] [-o str] fastx 478s 478s positional arguments: 478s fastx fastq file, gzip support 478s 478s options: 478s -h, --help show this help message and exit 478s -o, --out-file str output file, default: output to stdout 478s $ pyfastx subseq --help 478s usage: pyfastx subseq [-h] [-r str | -b str] [-o str] fastx [region ...] 478s 478s positional arguments: 478s fastx input fasta file, gzip support 478s region format is chr:start-end, start and end position is 478s 1-based, multiple regions were separated by space 478s 478s options: 478s -h, --help show this help message and exit 478s -r, --region-file str 478s tab-delimited file, one region per line, both start 478s and end position are 1-based 478s -b, --bed-file str tab-delimited BED file, 0-based start position and 478s 1-based end position 478s -o, --out-file str output file, default: output to stdout 478s $ pyfastx sample --help 478s usage: pyfastx sample [-h] (-n int | -p float) [-s int] [--sequential-read] 478s [-o str] 478s fastx 478s 478s positional arguments: 478s fastx fasta or fastq file, gzip support 478s 478s options: 478s -h, --help show this help message and exit 478s -n int number of sequences to be sampled 478s -p float proportion of sequences to be sampled, 0~1 478s -s, --seed int random seed, default is the current system time 478s --sequential-read start sequential reading, particularly suitable for 478s sampling large numbers of sequences 478s -o, --out-file str output file, default: output to stdout 478s $ pyfastx extract --help 478s usage: pyfastx extract [-h] [-l str] [--reverse-complement] [--out-fasta] 478s [-o str] [--sequential-read] 478s fastx [name ...] 478s 478s positional arguments: 478s fastx fasta or fastq file, gzip support 478s name sequence name or read name, multiple names were 478s separated by space 478s 478s options: 478s -h, --help show this help message and exit 478s -l, --list-file str a file containing sequence or read names, one name per 478s line 478s --reverse-complement output reverse complement sequence 478s --out-fasta output fasta format when extract reads from fastq, 478s default output fastq format 478s -o, --out-file str output file, default: output to stdout 478s --sequential-read start sequential reading, particularly suitable for 478s extracting large numbers of sequences 478s $ pyfastx --version 478s pyfastx version 2.2.0 478s $ pyfastx index protein.fa 478s $ pyfastx index rna.fa 479s $ pyfastx index test.fa 479s $ pyfastx index test.fq 479s $ pyfastx index test.fa.gz 479s $ pyfastx index test.fq.gz 479s $ pyfastx stat protein.fa 479s fileName seqType seqCounts totalBases GC% avgLen medianLen maxLen minLen N50 L50 479s protein.fa protein 17 2265 - 133.235 80.0 419 23 263 4 480s $ pyfastx split -n 2 protein.fa 480s $ pyfastx fq2fa test.fq -o test.fa 480s $ pyfastx subseq protein.fa UPI0000000011:1-4 480s >UPI0000000011:1-4 480s MVDA 480s $ pyfastx sample -n 1 test.fq.gz -o sample.fq 480s $ pyfastx extract protein.fa UPI0000000011 480s >UPI0000000011 status=active 480s MVDAITVLTAIGITVLMLLMVISGAAMIVKELNPNDIFTMQSLKFNRAVTIFKYIGLFIY 480s IPGTIILYATYVKSLLMKS 481s autopkgtest [15:40:19]: test test-cli: -----------------------] 485s autopkgtest [15:40:23]: test test-cli: - - - - - - - - - - results - - - - - - - - - - 485s test-cli PASS 489s autopkgtest [15:40:27]: @@@@@@@@@@@@@@@@@@@@ summary 489s run-unit-test PASS 489s test-cli PASS