1s autopkgtest [05:14:41]: starting date and time: 2024-03-14 05:14:41+0000 1s autopkgtest [05:14:41]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 1s autopkgtest [05:14:41]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.bmedaf7p/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:sqlite3,src:readline --apt-upgrade pyfastx --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=sqlite3/3.45.1-1ubuntu1 readline/8.2-3.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-s390x-20.secgroup --name adt-noble-s390x-pyfastx-20240314-051440-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 384s autopkgtest [05:21:04]: testbed dpkg architecture: s390x 384s autopkgtest [05:21:04]: testbed apt version: 2.7.12 384s autopkgtest [05:21:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup 385s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 386s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [47.2 kB] 386s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 386s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2891 kB] 387s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [453 kB] 387s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [595 kB] 387s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 387s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 387s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 387s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3156 kB] 388s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 388s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [27.7 kB] 388s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 390s Fetched 7303 kB in 3s (2395 kB/s) 390s Reading package lists... 393s Reading package lists... 394s Building dependency tree... 394s Reading state information... 394s Calculating upgrade... 394s The following packages will be upgraded: 394s dosfstools libsqlite3-0 readline-common 394s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 394s Need to get 895 kB of archives. 394s After this operation, 3072 B of additional disk space will be used. 394s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsqlite3-0 s390x 3.45.1-1ubuntu1 [747 kB] 395s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x readline-common all 8.2-3.1 [56.4 kB] 395s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x dosfstools s390x 4.2-1.1 [91.1 kB] 395s Fetched 895 kB in 1s (1603 kB/s) 395s (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 ... 52172 files and directories currently installed.) 395s Preparing to unpack .../libsqlite3-0_3.45.1-1ubuntu1_s390x.deb ... 395s Unpacking libsqlite3-0:s390x (3.45.1-1ubuntu1) over (3.45.1-1) ... 395s Preparing to unpack .../readline-common_8.2-3.1_all.deb ... 395s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 395s Preparing to unpack .../dosfstools_4.2-1.1_s390x.deb ... 395s Unpacking dosfstools (4.2-1.1) over (4.2-1build3) ... 395s Setting up libsqlite3-0:s390x (3.45.1-1ubuntu1) ... 395s Setting up dosfstools (4.2-1.1) ... 395s Setting up readline-common (8.2-3.1) ... 395s Processing triggers for man-db (2.12.0-3) ... 396s Processing triggers for install-info (7.1-3) ... 396s Processing triggers for libc-bin (2.39-0ubuntu2) ... 397s Reading package lists... 397s Building dependency tree... 397s Reading state information... 397s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 398s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 398s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 398s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 398s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 400s Reading package lists... 400s Reading package lists... 400s Building dependency tree... 400s Reading state information... 401s Calculating upgrade... 401s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 401s Reading package lists... 401s Building dependency tree... 401s Reading state information... 401s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 404s autopkgtest [05:21:24]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 404s autopkgtest [05:21:24]: @@@@@@@@@@@@@@@@@@@@ apt-source pyfastx 407s Get:1 http://ftpmaster.internal/ubuntu noble/universe pyfastx 2.0.2-2 (dsc) [2292 B] 407s Get:2 http://ftpmaster.internal/ubuntu noble/universe pyfastx 2.0.2-2 (tar) [230 kB] 407s Get:3 http://ftpmaster.internal/ubuntu noble/universe pyfastx 2.0.2-2 (diff) [33.6 kB] 407s gpgv: Signature made Wed Dec 13 10:25:09 2023 UTC 407s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 407s gpgv: issuer "emollier@debian.org" 407s gpgv: Can't check signature: No public key 407s dpkg-source: warning: cannot verify inline signature for ./pyfastx_2.0.2-2.dsc: no acceptable signature found 407s autopkgtest [05:21:27]: testing package pyfastx version 2.0.2-2 407s autopkgtest [05:21:27]: build not needed 408s autopkgtest [05:21:28]: test run-unit-test: preparing testbed 409s Reading package lists... 409s Building dependency tree... 409s Reading state information... 410s Starting pkgProblemResolver with broken count: 0 410s Starting 2 pkgProblemResolver with broken count: 0 410s Done 411s The following additional packages will be installed: 411s pyfastx python3-all python3-importlib-metadata python3-more-itertools 411s python3-pyfaidx python3-pyfastx python3-zipp 411s Recommended packages: 411s python3-biopython 411s The following NEW packages will be installed: 411s autopkgtest-satdep pyfastx python3-all python3-importlib-metadata 411s python3-more-itertools python3-pyfaidx python3-pyfastx python3-zipp 411s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 411s Need to get 300 kB/300 kB of archives. 411s After this operation, 993 kB of additional disk space will be used. 411s Get:1 /tmp/autopkgtest.71Uyex/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [716 B] 411s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x python3-more-itertools all 10.2.0-1 [52.9 kB] 411s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x python3-zipp all 1.0.0-6 [6090 B] 411s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x python3-importlib-metadata all 4.12.0-1 [17.8 kB] 411s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pyfaidx all 0.8.1.1-1 [29.6 kB] 411s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pyfastx s390x 2.0.2-2 [69.7 kB] 411s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x pyfastx s390x 2.0.2-2 [123 kB] 411s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x python3-all s390x 3.12.1-0ubuntu2 [908 B] 412s Fetched 300 kB in 0s (608 kB/s) 412s Selecting previously unselected package python3-more-itertools. 412s (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 ... 52171 files and directories currently installed.) 412s Preparing to unpack .../0-python3-more-itertools_10.2.0-1_all.deb ... 412s Unpacking python3-more-itertools (10.2.0-1) ... 412s Selecting previously unselected package python3-zipp. 412s Preparing to unpack .../1-python3-zipp_1.0.0-6_all.deb ... 412s Unpacking python3-zipp (1.0.0-6) ... 412s Selecting previously unselected package python3-importlib-metadata. 412s Preparing to unpack .../2-python3-importlib-metadata_4.12.0-1_all.deb ... 412s Unpacking python3-importlib-metadata (4.12.0-1) ... 412s Selecting previously unselected package python3-pyfaidx. 412s Preparing to unpack .../3-python3-pyfaidx_0.8.1.1-1_all.deb ... 412s Unpacking python3-pyfaidx (0.8.1.1-1) ... 412s Selecting previously unselected package python3-pyfastx. 412s Preparing to unpack .../4-python3-pyfastx_2.0.2-2_s390x.deb ... 412s Unpacking python3-pyfastx (2.0.2-2) ... 412s Selecting previously unselected package pyfastx. 412s Preparing to unpack .../5-pyfastx_2.0.2-2_s390x.deb ... 412s Unpacking pyfastx (2.0.2-2) ... 412s Selecting previously unselected package python3-all. 412s Preparing to unpack .../6-python3-all_3.12.1-0ubuntu2_s390x.deb ... 412s Unpacking python3-all (3.12.1-0ubuntu2) ... 412s Selecting previously unselected package autopkgtest-satdep. 412s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 412s Unpacking autopkgtest-satdep (0) ... 412s Setting up python3-more-itertools (10.2.0-1) ... 412s Setting up python3-all (3.12.1-0ubuntu2) ... 412s Setting up python3-zipp (1.0.0-6) ... 413s Setting up python3-importlib-metadata (4.12.0-1) ... 413s Setting up python3-pyfaidx (0.8.1.1-1) ... 413s Setting up python3-pyfastx (2.0.2-2) ... 413s Setting up pyfastx (2.0.2-2) ... 413s Setting up autopkgtest-satdep (0) ... 413s Processing triggers for man-db (2.12.0-3) ... 417s (Reading database ... 52268 files and directories currently installed.) 417s Removing autopkgtest-satdep (0) ... 417s autopkgtest [05:21:37]: test run-unit-test: [----------------------- 418s test_id_exception (tests.test_fakeys.IdentifierTest.test_id_exception) ... ok 418s test_key_identifier (tests.test_fakeys.IdentifierTest.test_key_identifier) ... ok 418s test_key_repr (tests.test_fakeys.IdentifierTest.test_key_repr) ... ok 418s test_key_slice (tests.test_fakeys.IdentifierTest.test_key_slice) ... ok 418s test_keys_filter (tests.test_fakeys.IdentifierTest.test_keys_filter) ... ok 418s test_keys_sort (tests.test_fakeys.IdentifierTest.test_keys_sort) ... ok 418s test_build (tests.test_fasta.FastaTest.test_build) ... ok 418s test_exception (tests.test_fasta.FastaTest.test_exception) ... ok 418s test_fasta (tests.test_fasta.FastaTest.test_fasta) ... ok 418s test_iter_full_name (tests.test_fasta.FastaTest.test_iter_full_name) ... ok 418s test_iter_object (tests.test_fasta.FastaTest.test_iter_object) ... ok 418s test_iter_tuple (tests.test_fasta.FastaTest.test_iter_tuple) ... ok 418s test_iter_upper (tests.test_fasta.FastaTest.test_iter_upper) ... ok 418s test_iter_upper_full_name (tests.test_fasta.FastaTest.test_iter_upper_full_name) ... ok 418s test_key_func (tests.test_fasta.FastaTest.test_key_func) ... ok 418s test_module (tests.test_fasta.FastaTest.test_module) ... ok 418s test_no_upper (tests.test_fasta.FastaTest.test_no_upper) ... ok 418s test_repr (tests.test_fasta.FastaTest.test_repr) ... ok 418s test_seq_fetch (tests.test_fasta.FastaTest.test_seq_fetch) ... ok 418s test_seq_flank (tests.test_fasta.FastaTest.test_seq_flank) ... ok 419s test_seq_type (tests.test_fasta.FastaTest.test_seq_type) ... ok 419s test_statistics (tests.test_fasta.FastaTest.test_statistics) ... ok 419s test_build (tests.test_fastq.FastqTest.test_build) ... ok 419s test_exception (tests.test_fastq.FastqTest.test_exception) ... ok 419s test_fastq (tests.test_fastq.FastqTest.test_fastq) ... ok 419s test_full_name (tests.test_fastq.FastqTest.test_full_name) ... ok 419s test_iter_object (tests.test_fastq.FastqTest.test_iter_object) ... ok 419s test_iter_tuple (tests.test_fastq.FastqTest.test_iter_tuple) ... ok 419s test_negative (tests.test_fastq.FastqTest.test_negative) ... ok 419s test_platform (tests.test_fastq.FastqTest.test_platform) ... ok 420s test_read_len (tests.test_fastq.FastqTest.test_read_len) ... ok 420s test_repr (tests.test_fastq.FastqTest.test_repr) ... ok 420s test_exception (tests.test_fastx.FastxTest.test_exception) ... ok 420s test_fasta_iter (tests.test_fastx.FastxTest.test_fasta_iter) ... ok 420s test_fasta_upper (tests.test_fastx.FastxTest.test_fasta_upper) ... ok 420s test_fastq_iter (tests.test_fastx.FastxTest.test_fastq_iter) ... ok 420s test_fastx_repr (tests.test_fastx.FastxTest.test_fastx_repr) ... ok 420s test_exception (tests.test_fqkeys.FastxTest.test_exception) ... ok 420s test_fastq_key (tests.test_fqkeys.FastxTest.test_fastq_key) ... ok 420s test_read (tests.test_read.ReadTest.test_read) ... ok 420s test_read_description (tests.test_read.ReadTest.test_read_description) ... ok 420s test_read_raw (tests.test_read.ReadTest.test_read_raw) ... ok 420s test_read_seq (tests.test_read.ReadTest.test_read_seq) ... ok 420s test_repr (tests.test_read.ReadTest.test_repr) ... ok 420s test_full_compo (tests.test_sequence.SequenceTest.test_full_compo) ... ok 420s test_seq_by_index (tests.test_sequence.SequenceTest.test_seq_by_index) ... ok 420s test_seq_by_key (tests.test_sequence.SequenceTest.test_seq_by_key) ... ok 420s test_seq_content (tests.test_sequence.SequenceTest.test_seq_content) ... ok 420s test_seq_exception (tests.test_sequence.SequenceTest.test_seq_exception) ... ok 420s test_seq_iter (tests.test_sequence.SequenceTest.test_seq_iter) ... ok 420s test_seq_raw (tests.test_sequence.SequenceTest.test_seq_raw) ... ok 420s test_seq_repr (tests.test_sequence.SequenceTest.test_seq_repr) ... ok 420s test_seq_reverse_complement (tests.test_sequence.SequenceTest.test_seq_reverse_complement) ... ok 420s test_seq_slice (tests.test_sequence.SequenceTest.test_seq_slice) ... ok 420s test_seq_by_index (tests.test_sequence_error.SequenceErrorTest.test_seq_by_index) ... ok 420s test_seq_by_key (tests.test_sequence_error.SequenceErrorTest.test_seq_by_key) ... pyfastx: 2.0.2; zlib: 1.3; sqlite: 3.44.2; zran: 1.7.0 420s ok 420s 420s ---------------------------------------------------------------------- 420s Ran 56 tests in 2.509s 420s 420s OK 421s autopkgtest [05:21:41]: test run-unit-test: -----------------------] 421s autopkgtest [05:21:41]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 421s run-unit-test PASS 421s autopkgtest [05:21:41]: test test-cli: preparing testbed 892s autopkgtest [05:29:32]: testbed dpkg architecture: s390x 892s autopkgtest [05:29:32]: testbed apt version: 2.7.12 892s autopkgtest [05:29:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 893s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 893s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [47.2 kB] 893s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 893s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2891 kB] 893s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [453 kB] 893s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [595 kB] 893s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 893s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 893s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 893s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3156 kB] 894s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 894s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [27.7 kB] 894s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 895s Fetched 7303 kB in 2s (3410 kB/s) 895s Reading package lists... 898s Reading package lists... 898s Building dependency tree... 898s Reading state information... 898s Calculating upgrade... 898s The following packages will be upgraded: 898s dosfstools libsqlite3-0 readline-common 898s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 898s Need to get 895 kB of archives. 898s After this operation, 3072 B of additional disk space will be used. 898s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsqlite3-0 s390x 3.45.1-1ubuntu1 [747 kB] 899s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x readline-common all 8.2-3.1 [56.4 kB] 899s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x dosfstools s390x 4.2-1.1 [91.1 kB] 899s Fetched 895 kB in 1s (1661 kB/s) 899s (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 ... 52172 files and directories currently installed.) 899s Preparing to unpack .../libsqlite3-0_3.45.1-1ubuntu1_s390x.deb ... 899s Unpacking libsqlite3-0:s390x (3.45.1-1ubuntu1) over (3.45.1-1) ... 899s Preparing to unpack .../readline-common_8.2-3.1_all.deb ... 899s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 899s Preparing to unpack .../dosfstools_4.2-1.1_s390x.deb ... 899s Unpacking dosfstools (4.2-1.1) over (4.2-1build3) ... 899s Setting up libsqlite3-0:s390x (3.45.1-1ubuntu1) ... 899s Setting up dosfstools (4.2-1.1) ... 899s Setting up readline-common (8.2-3.1) ... 899s Processing triggers for man-db (2.12.0-3) ... 899s Processing triggers for install-info (7.1-3) ... 899s Processing triggers for libc-bin (2.39-0ubuntu2) ... 900s Reading package lists... 900s Building dependency tree... 900s Reading state information... 900s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 900s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 900s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 900s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 901s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 902s Reading package lists... 902s Reading package lists... 902s Building dependency tree... 902s Reading state information... 902s Calculating upgrade... 902s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 902s Reading package lists... 902s Building dependency tree... 902s Reading state information... 902s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 909s Reading package lists... 909s Building dependency tree... 909s Reading state information... 910s Starting pkgProblemResolver with broken count: 0 910s Starting 2 pkgProblemResolver with broken count: 0 910s Done 910s The following additional packages will be installed: 910s pyfastx python3-importlib-metadata python3-more-itertools python3-pyfaidx 910s python3-pyfastx python3-zipp 910s Recommended packages: 910s python3-biopython 910s The following NEW packages will be installed: 910s autopkgtest-satdep pyfastx python3-importlib-metadata python3-more-itertools 910s python3-pyfaidx python3-pyfastx python3-zipp 910s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 910s Need to get 299 kB/299 kB of archives. 910s After this operation, 987 kB of additional disk space will be used. 910s Get:1 /tmp/autopkgtest.71Uyex/2-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [712 B] 910s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x python3-more-itertools all 10.2.0-1 [52.9 kB] 910s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x python3-zipp all 1.0.0-6 [6090 B] 910s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x python3-importlib-metadata all 4.12.0-1 [17.8 kB] 910s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pyfaidx all 0.8.1.1-1 [29.6 kB] 910s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pyfastx s390x 2.0.2-2 [69.7 kB] 910s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x pyfastx s390x 2.0.2-2 [123 kB] 911s Fetched 299 kB in 1s (450 kB/s) 911s Selecting previously unselected package python3-more-itertools. 911s (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 ... 52171 files and directories currently installed.) 911s Preparing to unpack .../0-python3-more-itertools_10.2.0-1_all.deb ... 911s Unpacking python3-more-itertools (10.2.0-1) ... 911s Selecting previously unselected package python3-zipp. 911s Preparing to unpack .../1-python3-zipp_1.0.0-6_all.deb ... 911s Unpacking python3-zipp (1.0.0-6) ... 911s Selecting previously unselected package python3-importlib-metadata. 911s Preparing to unpack .../2-python3-importlib-metadata_4.12.0-1_all.deb ... 911s Unpacking python3-importlib-metadata (4.12.0-1) ... 911s Selecting previously unselected package python3-pyfaidx. 911s Preparing to unpack .../3-python3-pyfaidx_0.8.1.1-1_all.deb ... 911s Unpacking python3-pyfaidx (0.8.1.1-1) ... 911s Selecting previously unselected package python3-pyfastx. 911s Preparing to unpack .../4-python3-pyfastx_2.0.2-2_s390x.deb ... 911s Unpacking python3-pyfastx (2.0.2-2) ... 911s Selecting previously unselected package pyfastx. 911s Preparing to unpack .../5-pyfastx_2.0.2-2_s390x.deb ... 911s Unpacking pyfastx (2.0.2-2) ... 911s Selecting previously unselected package autopkgtest-satdep. 911s Preparing to unpack .../6-2-autopkgtest-satdep.deb ... 911s Unpacking autopkgtest-satdep (0) ... 911s Setting up python3-more-itertools (10.2.0-1) ... 911s Setting up python3-zipp (1.0.0-6) ... 911s Setting up python3-importlib-metadata (4.12.0-1) ... 911s Setting up python3-pyfaidx (0.8.1.1-1) ... 911s Setting up python3-pyfastx (2.0.2-2) ... 911s Setting up pyfastx (2.0.2-2) ... 911s Setting up autopkgtest-satdep (0) ... 911s Processing triggers for man-db (2.12.0-3) ... 914s (Reading database ... 52267 files and directories currently installed.) 914s Removing autopkgtest-satdep (0) ... 915s autopkgtest [05:29:55]: test test-cli: [----------------------- 916s $ pyfastx --help 916s usage: pyfastx COMMAND [OPTIONS] 916s 916s A command line tool for FASTA/Q file manipulation 916s 916s options: 916s -h, --help show this help message and exit 916s -v, --version show program's version number and exit 916s 916s Commands: 916s 916s index build index for fasta/q file 916s stat show detailed statistics information of fasta/q file 916s split split fasta/q file into multiple files 916s fq2fa convert fastq file to fasta file 916s subseq get subsequences from fasta file by region 916s sample randomly sample sequences from fasta or fastq file 916s extract extract full sequences or reads from fasta/q file 916s $ # Found pyfastx commands: 'index stat split fq2fa subseq sample extract' 916s $ pyfastx index --help 916s usage: pyfastx index [-h] [-f] fastx [fastx ...] 916s 916s positional arguments: 916s fastx fasta or fastq file, gzip support 916s 916s options: 916s -h, --help show this help message and exit 916s -f, --full build full index, base composition will be calculated 916s $ pyfastx stat --help 916s usage: pyfastx stat [-h] fastx [fastx ...] 916s 916s positional arguments: 916s fastx fasta or fastq file, gzip support 916s 916s options: 916s -h, --help show this help message and exit 916s $ pyfastx split --help 916s usage: pyfastx split [-h] (-n int | -c int) [-o str] fastx 916s 916s positional arguments: 916s fastx fasta or fastq file, gzip support 916s 916s options: 916s -h, --help show this help message and exit 916s -n int split a fasta/q file into N new files with even size 916s -c int split a fasta/q file into multiple files containing 916s the same sequence counts 916s -o str, --out-dir str 916s output directory, default is current folder 916s $ pyfastx fq2fa --help 916s usage: pyfastx fq2fa [-h] [-o str] fastx 916s 916s positional arguments: 916s fastx fastq file, gzip support 916s 916s options: 916s -h, --help show this help message and exit 916s -o str, --out-file str 916s output file, default: output to stdout 916s $ pyfastx subseq --help 916s usage: pyfastx subseq [-h] [-r str | -b str] [-o str] fastx [region ...] 916s 916s positional arguments: 916s fastx input fasta file, gzip support 916s region format is chr:start-end, start and end position is 916s 1-based, multiple regions were separated by space 916s 916s options: 916s -h, --help show this help message and exit 916s -r str, --region-file str 916s tab-delimited file, one region per line, both start 916s and end position are 1-based 916s -b str, --bed-file str 916s tab-delimited BED file, 0-based start position and 916s 1-based end position 916s -o str, --out-file str 916s output file, default: output to stdout 916s $ pyfastx sample --help 916s usage: pyfastx sample [-h] (-n int | -p float) [-s int] [--sequential-read] 916s [-o str] 916s fastx 916s 916s positional arguments: 916s fastx fasta or fastq file, gzip support 916s 916s options: 916s -h, --help show this help message and exit 916s -n int number of sequences to be sampled 916s -p float proportion of sequences to be sampled, 0~1 916s -s int, --seed int random seed, default is the current system time 916s --sequential-read start sequential reading, particularly suitable for 916s sampling large numbers of sequences 916s -o str, --out-file str 916s output file, default: output to stdout 916s $ pyfastx extract --help 916s usage: pyfastx extract [-h] [-l str] [--reverse-complement] [--out-fasta] 916s [-o str] [--sequential-read] 916s fastx [name ...] 916s 916s positional arguments: 916s fastx fasta or fastq file, gzip support 916s name sequence name or read name, multiple names were 916s separated by space 916s 916s options: 916s -h, --help show this help message and exit 916s -l str, --list-file str 916s a file containing sequence or read names, one name per 916s line 916s --reverse-complement output reverse complement sequence 916s --out-fasta output fasta format when extract reads from fastq, 916s default output fastq format 916s -o str, --out-file str 916s output file, default: output to stdout 916s --sequential-read start sequential reading, particularly suitable for 916s extracting large numbers of sequences 916s $ pyfastx --version 916s pyfastx version 2.0.2 916s $ pyfastx index protein.fa 916s $ pyfastx index rna.fa 916s $ pyfastx index test.fa 916s $ pyfastx index test.fq 916s $ pyfastx index test.fa.gz 917s $ pyfastx index test.fq.gz 917s $ pyfastx stat protein.fa 917s fileName seqType seqCounts totalBases GC% avgLen medianLen maxLen minLen N50 L50 917s protein.fa protein 17 2265 - 133.235 80.0 419 23 263 4 917s $ pyfastx split -n 2 protein.fa 917s $ pyfastx fq2fa test.fq -o test.fa 917s $ pyfastx subseq protein.fa UPI0000000011:1-4 917s >UPI0000000011:1-4 917s MVDA 917s $ pyfastx sample -n 1 test.fq.gz -o sample.fq 917s $ pyfastx extract protein.fa UPI0000000011 917s >UPI0000000011 status=active 917s MVDAITVLTAIGITVLMLLMVISGAAMIVKELNPNDIFTMQSLKFNRAVTIFKYIGLFIY 917s IPGTIILYATYVKSLLMKS 918s autopkgtest [05:29:58]: test test-cli: -----------------------] 918s test-cli PASS 918s autopkgtest [05:29:58]: test test-cli: - - - - - - - - - - results - - - - - - - - - - 918s autopkgtest [05:29:58]: @@@@@@@@@@@@@@@@@@@@ summary 918s run-unit-test PASS 918s test-cli PASS 930s Creating nova instance adt-noble-s390x-pyfastx-20240314-051440-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240314.img (UUID fb64e3af-fc57-4dd0-8211-8847198de92f)... 930s Creating nova instance adt-noble-s390x-pyfastx-20240314-051440-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240314.img (UUID fb64e3af-fc57-4dd0-8211-8847198de92f)...