0s autopkgtest [12:29:07]: starting date and time: 2024-11-13 12:29:07+0000 0s autopkgtest [12:29:07]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [12:29:07]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8ca1vby2/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade pyfastx --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-18.secgroup --name adt-plucky-s390x-pyfastx-20241113-122906-juju-7f2275-prod-proposed-migration-environment-20-e0234dd7-cf0e-441e-8295-2283d85365a2 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -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://ftpmaster.internal/ubuntu/ 104s autopkgtest [12:30:51]: testbed dpkg architecture: s390x 104s autopkgtest [12:30:51]: testbed apt version: 2.9.8 104s autopkgtest [12:30:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup 105s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 105s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.5 kB] 105s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 105s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 105s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [967 kB] 105s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [107 kB] 105s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [641 kB] 105s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [17.4 kB] 105s Fetched 1934 kB in 1s (2352 kB/s) 105s Reading package lists... 107s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Calculating upgrade... 108s The following NEW packages will be installed: 108s python3.13-gdbm 108s The following packages will be upgraded: 108s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 108s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 108s Need to get 252 kB of archives. 108s After this operation, 98.3 kB of additional disk space will be used. 108s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-minimal s390x 3.12.7-1 [27.4 kB] 108s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3 s390x 3.12.7-1 [24.0 kB] 108s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-stdlib s390x 3.12.7-1 [10.0 kB] 108s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-gdbm s390x 3.13.0-2 [31.0 kB] 108s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-gdbm s390x 3.12.7-1 [8642 B] 108s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libgpgme11t64 s390x 1.23.2-5ubuntu4 [151 kB] 108s Fetched 252 kB in 0s (598 kB/s) 109s (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 ... 55510 files and directories currently installed.) 109s Preparing to unpack .../python3-minimal_3.12.7-1_s390x.deb ... 109s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 109s Setting up python3-minimal (3.12.7-1) ... 109s (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 ... 55510 files and directories currently installed.) 109s Preparing to unpack .../python3_3.12.7-1_s390x.deb ... 109s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 109s Preparing to unpack .../libpython3-stdlib_3.12.7-1_s390x.deb ... 109s Unpacking libpython3-stdlib:s390x (3.12.7-1) over (3.12.6-0ubuntu1) ... 109s Selecting previously unselected package python3.13-gdbm. 109s Preparing to unpack .../python3.13-gdbm_3.13.0-2_s390x.deb ... 109s Unpacking python3.13-gdbm (3.13.0-2) ... 109s Preparing to unpack .../python3-gdbm_3.12.7-1_s390x.deb ... 109s Unpacking python3-gdbm:s390x (3.12.7-1) over (3.12.6-1ubuntu1) ... 109s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_s390x.deb ... 109s Unpacking libgpgme11t64:s390x (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 109s Setting up libgpgme11t64:s390x (1.23.2-5ubuntu4) ... 109s Setting up python3.13-gdbm (3.13.0-2) ... 109s Setting up libpython3-stdlib:s390x (3.12.7-1) ... 109s Setting up python3 (3.12.7-1) ... 109s Setting up python3-gdbm:s390x (3.12.7-1) ... 109s Processing triggers for man-db (2.12.1-3) ... 110s Processing triggers for libc-bin (2.40-1ubuntu3) ... 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 111s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 111s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 111s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 111s Reading package lists... 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 112s Calculating upgrade... 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s autopkgtest [12:31:01]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 115s autopkgtest [12:31:02]: @@@@@@@@@@@@@@@@@@@@ apt-source pyfastx 117s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (dsc) [2289 B] 117s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (tar) [230 kB] 117s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (diff) [7412 B] 117s gpgv: Signature made Fri Aug 30 18:49:12 2024 UTC 117s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 117s gpgv: issuer "emollier@debian.org" 117s gpgv: Can't check signature: No public key 117s dpkg-source: warning: cannot verify inline signature for ./pyfastx_2.1.0-2.dsc: no acceptable signature found 117s autopkgtest [12:31:04]: testing package pyfastx version 2.1.0-2 117s autopkgtest [12:31:04]: build not needed 117s autopkgtest [12:31:04]: test run-unit-test: preparing testbed 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s Starting pkgProblemResolver with broken count: 0 119s Starting 2 pkgProblemResolver with broken count: 0 119s Done 119s The following additional packages will be installed: 119s libpython3.13-minimal libpython3.13-stdlib pyfastx python3-all 119s python3-importlib-metadata python3-packaging python3-pyfaidx python3-pyfastx 119s python3.13 python3.13-minimal 119s Suggested packages: 119s python3.13-venv python3.13-doc binfmt-support 119s Recommended packages: 119s python3-biopython 119s The following NEW packages will be installed: 119s autopkgtest-satdep libpython3.13-minimal libpython3.13-stdlib pyfastx 119s python3-all python3-importlib-metadata python3-packaging python3-pyfaidx 119s python3-pyfastx python3.13 python3.13-minimal 119s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 119s Need to get 6128 kB/6128 kB of archives. 119s After this operation, 23.2 MB of additional disk space will be used. 119s Get:1 /tmp/autopkgtest.5hiHJ3/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [716 B] 119s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-minimal s390x 3.13.0-2 [877 kB] 120s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-minimal s390x 3.13.0-2 [2172 kB] 120s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-stdlib s390x 3.13.0-2 [2086 kB] 120s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x python3-importlib-metadata all 8.5.0-1 [20.7 kB] 120s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x python3-packaging all 24.1-1 [41.4 kB] 120s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 120s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyfastx s390x 2.1.0-2 [58.8 kB] 120s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x pyfastx s390x 2.1.0-2 [122 kB] 120s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13 s390x 3.13.0-2 [719 kB] 120s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-all s390x 3.12.7-1 [890 B] 120s Fetched 6128 kB in 1s (7653 kB/s) 120s Selecting previously unselected package libpython3.13-minimal:s390x. 120s (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 ... 55517 files and directories currently installed.) 120s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_s390x.deb ... 120s Unpacking libpython3.13-minimal:s390x (3.13.0-2) ... 120s Selecting previously unselected package python3.13-minimal. 120s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_s390x.deb ... 120s Unpacking python3.13-minimal (3.13.0-2) ... 120s Selecting previously unselected package libpython3.13-stdlib:s390x. 120s Preparing to unpack .../02-libpython3.13-stdlib_3.13.0-2_s390x.deb ... 120s Unpacking libpython3.13-stdlib:s390x (3.13.0-2) ... 120s Selecting previously unselected package python3-importlib-metadata. 120s Preparing to unpack .../03-python3-importlib-metadata_8.5.0-1_all.deb ... 120s Unpacking python3-importlib-metadata (8.5.0-1) ... 120s Selecting previously unselected package python3-packaging. 120s Preparing to unpack .../04-python3-packaging_24.1-1_all.deb ... 120s Unpacking python3-packaging (24.1-1) ... 120s Selecting previously unselected package python3-pyfaidx. 120s Preparing to unpack .../05-python3-pyfaidx_0.8.1.3-1_all.deb ... 120s Unpacking python3-pyfaidx (0.8.1.3-1) ... 120s Selecting previously unselected package python3-pyfastx. 120s Preparing to unpack .../06-python3-pyfastx_2.1.0-2_s390x.deb ... 120s Unpacking python3-pyfastx (2.1.0-2) ... 120s Selecting previously unselected package pyfastx. 120s Preparing to unpack .../07-pyfastx_2.1.0-2_s390x.deb ... 120s Unpacking pyfastx (2.1.0-2) ... 120s Selecting previously unselected package python3.13. 120s Preparing to unpack .../08-python3.13_3.13.0-2_s390x.deb ... 120s Unpacking python3.13 (3.13.0-2) ... 120s Selecting previously unselected package python3-all. 120s Preparing to unpack .../09-python3-all_3.12.7-1_s390x.deb ... 120s Unpacking python3-all (3.12.7-1) ... 120s Selecting previously unselected package autopkgtest-satdep. 120s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 120s Unpacking autopkgtest-satdep (0) ... 121s Setting up python3-importlib-metadata (8.5.0-1) ... 121s Setting up libpython3.13-minimal:s390x (3.13.0-2) ... 121s Setting up python3-packaging (24.1-1) ... 121s Setting up python3.13-minimal (3.13.0-2) ... 122s Setting up libpython3.13-stdlib:s390x (3.13.0-2) ... 122s Setting up python3-pyfaidx (0.8.1.3-1) ... 122s Setting up python3.13 (3.13.0-2) ... 123s Setting up python3-pyfastx (2.1.0-2) ... 123s Setting up python3-all (3.12.7-1) ... 123s Setting up pyfastx (2.1.0-2) ... 123s Setting up autopkgtest-satdep (0) ... 123s Processing triggers for man-db (2.12.1-3) ... 123s Processing triggers for systemd (256.5-2ubuntu4) ... 125s (Reading database ... 56349 files and directories currently installed.) 125s Removing autopkgtest-satdep (0) ... 126s autopkgtest [12:31:13]: test run-unit-test: [----------------------- 126s tests.test_fakeys (unittest.loader._FailedTest.tests.test_fakeys) ... ERROR 126s tests.test_fasta (unittest.loader._FailedTest.tests.test_fasta) ... ERROR 126s tests.test_fastq (unittest.loader._FailedTest.tests.test_fastq) ... ERROR 126s tests.test_fastx (unittest.loader._FailedTest.tests.test_fastx) ... ERROR 126s tests.test_fqkeys (unittest.loader._FailedTest.tests.test_fqkeys) ... ERROR 126s tests.test_read (unittest.loader._FailedTest.tests.test_read) ... ERROR 126s tests.test_sequence (unittest.loader._FailedTest.tests.test_sequence) ... ERROR 126s tests.test_sequence_error (unittest.loader._FailedTest.tests.test_sequence_error) ... ERROR 126s 126s ====================================================================== 126s ERROR: tests.test_fakeys (unittest.loader._FailedTest.tests.test_fakeys) 126s ---------------------------------------------------------------------- 126s ImportError: Failed to import test module: tests.test_fakeys 126s Traceback (most recent call last): 126s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 126s module = self._get_module_from_name(name) 126s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 126s __import__(name) 126s ~~~~~~~~~~^^^^^^ 126s File "/tmp/autopkgtest.5hiHJ3/build.2b4/src/tests/test_fakeys.py", line 3, in 126s import pyfastx 126s ModuleNotFoundError: No module named 'pyfastx' 126s 126s 126s ====================================================================== 126s ERROR: tests.test_fasta (unittest.loader._FailedTest.tests.test_fasta) 126s ---------------------------------------------------------------------- 126s ImportError: Failed to import test module: tests.test_fasta 126s Traceback (most recent call last): 126s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 126s module = self._get_module_from_name(name) 126s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 126s __import__(name) 126s ~~~~~~~~~~^^^^^^ 126s File "/tmp/autopkgtest.5hiHJ3/build.2b4/src/tests/test_fasta.py", line 3, in 126s import pyfastx 126s ModuleNotFoundError: No module named 'pyfastx' 126s 126s 126s ====================================================================== 126s ERROR: tests.test_fastq (unittest.loader._FailedTest.tests.test_fastq) 126s ---------------------------------------------------------------------- 126s ImportError: Failed to import test module: tests.test_fastq 126s Traceback (most recent call last): 126s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 126s module = self._get_module_from_name(name) 126s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 126s __import__(name) 126s ~~~~~~~~~~^^^^^^ 126s File "/tmp/autopkgtest.5hiHJ3/build.2b4/src/tests/test_fastq.py", line 3, in 126s import pyfastx 126s ModuleNotFoundError: No module named 'pyfastx' 126s 126s 126s ====================================================================== 126s ERROR: tests.test_fastx (unittest.loader._FailedTest.tests.test_fastx) 126s ---------------------------------------------------------------------- 126s ImportError: Failed to import test module: tests.test_fastx 126s Traceback (most recent call last): 126s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 126s module = self._get_module_from_name(name) 126s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 126s __import__(name) 126s ~~~~~~~~~~^^^^^^ 126s File "/tmp/autopkgtest.5hiHJ3/build.2b4/src/tests/test_fastx.py", line 3, in 126s import pyfastx 126s ModuleNotFoundError: No module named 'pyfastx' 126s 126s 126s ====================================================================== 126s ERROR: tests.test_fqkeys (unittest.loader._FailedTest.tests.test_fqkeys) 126s ---------------------------------------------------------------------- 126s ImportError: Failed to import test module: tests.test_fqkeys 126s Traceback (most recent call last): 126s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 126s module = self._get_module_from_name(name) 126s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 126s __import__(name) 126s ~~~~~~~~~~^^^^^^ 126s File "/tmp/autopkgtest.5hiHJ3/build.2b4/src/tests/test_fqkeys.py", line 3, in 126s import pyfastx 126s ModuleNotFoundError: No module named 'pyfastx' 126s 126s 126s ====================================================================== 126s ERROR: tests.test_read (unittest.loader._FailedTest.tests.test_read) 126s ---------------------------------------------------------------------- 126s ImportError: Failed to import test module: tests.test_read 126s Traceback (most recent call last): 126s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 126s module = self._get_module_from_name(name) 126s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 126s __import__(name) 126s ~~~~~~~~~~^^^^^^ 126s File "/tmp/autopkgtest.5hiHJ3/build.2b4/src/tests/test_read.py", line 4, in 126s import pyfastx 126s ModuleNotFoundError: No module named 'pyfastx' 126s 126s 126s ====================================================================== 126s ERROR: tests.test_sequence (unittest.loader._FailedTest.tests.test_sequence) 126s ---------------------------------------------------------------------- 126s ImportError: Failed to import test module: tests.test_sequence 126s Traceback (most recent call last): 126s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 126s module = self._get_module_from_name(name) 126s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 126s __import__(name) 126s ~~~~~~~~~~^^^^^^ 126s File "/tmp/autopkgtest.5hiHJ3/build.2b4/src/tests/test_sequence.py", line 3, in 126s import pyfastx 126s ModuleNotFoundError: No module named 'pyfastx' 126s 126s 126s ====================================================================== 126s ERROR: tests.test_sequence_error (unittest.loader._FailedTest.tests.test_sequence_error) 126s ---------------------------------------------------------------------- 126s ImportError: Failed to import test module: tests.test_sequence_error 126s Traceback (most recent call last): 126s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 126s module = self._get_module_from_name(name) 126s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 126s __import__(name) 126s ~~~~~~~~~~^^^^^^ 126s File "/tmp/autopkgtest.5hiHJ3/build.2b4/src/tests/test_sequence_error.py", line 3, in 126s import pyfastx 126s ModuleNotFoundError: No module named 'pyfastx' 126s 126s 126s ---------------------------------------------------------------------- 126s Ran 8 tests in 0.001s 126s 126s FAILED (errors=8) 126s autopkgtest [12:31:13]: test run-unit-test: -----------------------] 127s autopkgtest [12:31:14]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 127s run-unit-test FAIL non-zero exit status 1 127s autopkgtest [12:31:14]: test test-cli: preparing testbed 244s autopkgtest [12:33:11]: testbed dpkg architecture: s390x 244s autopkgtest [12:33:11]: testbed apt version: 2.9.8 244s autopkgtest [12:33:11]: @@@@@@@@@@@@@@@@@@@@ test bed setup 244s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 245s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 245s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 245s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [967 kB] 245s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.5 kB] 245s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [107 kB] 245s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [641 kB] 245s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [17.4 kB] 245s Fetched 1934 kB in 1s (2396 kB/s) 245s Reading package lists... 247s Reading package lists... 247s Building dependency tree... 247s Reading state information... 247s Calculating upgrade... 248s The following NEW packages will be installed: 248s python3.13-gdbm 248s The following packages will be upgraded: 248s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 248s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 248s Need to get 252 kB of archives. 248s After this operation, 98.3 kB of additional disk space will be used. 248s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-minimal s390x 3.12.7-1 [27.4 kB] 248s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3 s390x 3.12.7-1 [24.0 kB] 248s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-stdlib s390x 3.12.7-1 [10.0 kB] 248s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-gdbm s390x 3.13.0-2 [31.0 kB] 248s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-gdbm s390x 3.12.7-1 [8642 B] 248s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libgpgme11t64 s390x 1.23.2-5ubuntu4 [151 kB] 248s Fetched 252 kB in 0s (584 kB/s) 248s (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 ... 55510 files and directories currently installed.) 248s Preparing to unpack .../python3-minimal_3.12.7-1_s390x.deb ... 248s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 248s Setting up python3-minimal (3.12.7-1) ... 249s (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 ... 55510 files and directories currently installed.) 249s Preparing to unpack .../python3_3.12.7-1_s390x.deb ... 249s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 249s Preparing to unpack .../libpython3-stdlib_3.12.7-1_s390x.deb ... 249s Unpacking libpython3-stdlib:s390x (3.12.7-1) over (3.12.6-0ubuntu1) ... 249s Selecting previously unselected package python3.13-gdbm. 249s Preparing to unpack .../python3.13-gdbm_3.13.0-2_s390x.deb ... 249s Unpacking python3.13-gdbm (3.13.0-2) ... 249s Preparing to unpack .../python3-gdbm_3.12.7-1_s390x.deb ... 249s Unpacking python3-gdbm:s390x (3.12.7-1) over (3.12.6-1ubuntu1) ... 249s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_s390x.deb ... 249s Unpacking libgpgme11t64:s390x (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 249s Setting up libgpgme11t64:s390x (1.23.2-5ubuntu4) ... 249s Setting up python3.13-gdbm (3.13.0-2) ... 249s Setting up libpython3-stdlib:s390x (3.12.7-1) ... 249s Setting up python3 (3.12.7-1) ... 249s Setting up python3-gdbm:s390x (3.12.7-1) ... 249s Processing triggers for man-db (2.12.1-3) ... 249s Processing triggers for libc-bin (2.40-1ubuntu3) ... 250s Reading package lists... 250s Building dependency tree... 250s Reading state information... 250s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 250s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 250s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 250s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 250s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 251s Reading package lists... 251s Reading package lists... 251s Building dependency tree... 251s Reading state information... 251s Calculating upgrade... 252s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 252s Reading package lists... 252s Building dependency tree... 252s Reading state information... 252s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 256s Reading package lists... 257s Building dependency tree... 257s Reading state information... 257s Starting pkgProblemResolver with broken count: 0 257s Starting 2 pkgProblemResolver with broken count: 0 257s Done 257s The following additional packages will be installed: 257s pyfastx python3-importlib-metadata python3-packaging python3-pyfaidx 257s python3-pyfastx 257s Recommended packages: 257s python3-biopython 257s The following NEW packages will be installed: 257s autopkgtest-satdep pyfastx python3-importlib-metadata python3-packaging 257s python3-pyfaidx python3-pyfastx 257s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 257s Need to get 272 kB/273 kB of archives. 257s After this operation, 762 kB of additional disk space will be used. 257s Get:1 /tmp/autopkgtest.5hiHJ3/2-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [712 B] 257s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x python3-importlib-metadata all 8.5.0-1 [20.7 kB] 257s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-packaging all 24.1-1 [41.4 kB] 257s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 257s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyfastx s390x 2.1.0-2 [58.8 kB] 257s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x pyfastx s390x 2.1.0-2 [122 kB] 258s Fetched 272 kB in 0s (559 kB/s) 258s Selecting previously unselected package python3-importlib-metadata. 258s (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 ... 55517 files and directories currently installed.) 258s Preparing to unpack .../0-python3-importlib-metadata_8.5.0-1_all.deb ... 258s Unpacking python3-importlib-metadata (8.5.0-1) ... 258s Selecting previously unselected package python3-packaging. 258s Preparing to unpack .../1-python3-packaging_24.1-1_all.deb ... 258s Unpacking python3-packaging (24.1-1) ... 258s Selecting previously unselected package python3-pyfaidx. 258s Preparing to unpack .../2-python3-pyfaidx_0.8.1.3-1_all.deb ... 258s Unpacking python3-pyfaidx (0.8.1.3-1) ... 258s Selecting previously unselected package python3-pyfastx. 258s Preparing to unpack .../3-python3-pyfastx_2.1.0-2_s390x.deb ... 258s Unpacking python3-pyfastx (2.1.0-2) ... 258s Selecting previously unselected package pyfastx. 258s Preparing to unpack .../4-pyfastx_2.1.0-2_s390x.deb ... 258s Unpacking pyfastx (2.1.0-2) ... 258s Selecting previously unselected package autopkgtest-satdep. 258s Preparing to unpack .../5-2-autopkgtest-satdep.deb ... 258s Unpacking autopkgtest-satdep (0) ... 258s Setting up python3-importlib-metadata (8.5.0-1) ... 258s Setting up python3-packaging (24.1-1) ... 258s Setting up python3-pyfaidx (0.8.1.3-1) ... 258s Setting up python3-pyfastx (2.1.0-2) ... 258s Setting up pyfastx (2.1.0-2) ... 258s Setting up autopkgtest-satdep (0) ... 258s Processing triggers for man-db (2.12.1-3) ... 260s (Reading database ... 55614 files and directories currently installed.) 260s Removing autopkgtest-satdep (0) ... 262s autopkgtest [12:33:29]: test test-cli: [----------------------- 262s $ pyfastx --help 262s usage: pyfastx COMMAND [OPTIONS] 262s 262s A command line tool for FASTA/Q file manipulation 262s 262s options: 262s -h, --help show this help message and exit 262s -v, --version show program's version number and exit 262s 262s Commands: 262s 262s index build index for fasta/q file 262s stat show detailed statistics information of fasta/q file 262s split split fasta/q file into multiple files 262s fq2fa convert fastq file to fasta file 262s subseq get subsequences from fasta file by region 262s sample randomly sample sequences from fasta or fastq file 262s extract extract full sequences or reads from fasta/q file 262s $ # Found pyfastx commands: 'index stat split fq2fa subseq sample extract' 262s $ pyfastx index --help 262s usage: pyfastx index [-h] [-f] fastx [fastx ...] 262s 262s positional arguments: 262s fastx fasta or fastq file, gzip support 262s 262s options: 262s -h, --help show this help message and exit 262s -f, --full build full index, base composition will be calculated 262s $ pyfastx stat --help 262s usage: pyfastx stat [-h] fastx [fastx ...] 262s 262s positional arguments: 262s fastx fasta or fastq file, gzip support 262s 262s options: 262s -h, --help show this help message and exit 262s $ pyfastx split --help 262s usage: pyfastx split [-h] (-n int | -c int) [-o str] fastx 262s 262s positional arguments: 262s fastx fasta or fastq file, gzip support 262s 262s options: 262s -h, --help show this help message and exit 262s -n int split a fasta/q file into N new files with even size 262s -c int split a fasta/q file into multiple files containing 262s the same sequence counts 262s -o str, --out-dir str 262s output directory, default is current folder 262s $ pyfastx fq2fa --help 263s usage: pyfastx fq2fa [-h] [-o str] fastx 263s 263s positional arguments: 263s fastx fastq file, gzip support 263s 263s options: 263s -h, --help show this help message and exit 263s -o str, --out-file str 263s output file, default: output to stdout 263s $ pyfastx subseq --help 263s usage: pyfastx subseq [-h] [-r str | -b str] [-o str] fastx [region ...] 263s 263s positional arguments: 263s fastx input fasta file, gzip support 263s region format is chr:start-end, start and end position is 263s 1-based, multiple regions were separated by space 263s 263s options: 263s -h, --help show this help message and exit 263s -r str, --region-file str 263s tab-delimited file, one region per line, both start 263s and end position are 1-based 263s -b str, --bed-file str 263s tab-delimited BED file, 0-based start position and 263s 1-based end position 263s -o str, --out-file str 263s output file, default: output to stdout 263s $ pyfastx sample --help 263s usage: pyfastx sample [-h] (-n int | -p float) [-s int] [--sequential-read] 263s [-o str] 263s fastx 263s 263s positional arguments: 263s fastx fasta or fastq file, gzip support 263s 263s options: 263s -h, --help show this help message and exit 263s -n int number of sequences to be sampled 263s -p float proportion of sequences to be sampled, 0~1 263s -s int, --seed int random seed, default is the current system time 263s --sequential-read start sequential reading, particularly suitable for 263s sampling large numbers of sequences 263s -o str, --out-file str 263s output file, default: output to stdout 263s $ pyfastx extract --help 263s usage: pyfastx extract [-h] [-l str] [--reverse-complement] [--out-fasta] 263s [-o str] [--sequential-read] 263s fastx [name ...] 263s 263s positional arguments: 263s fastx fasta or fastq file, gzip support 263s name sequence name or read name, multiple names were 263s separated by space 263s 263s options: 263s -h, --help show this help message and exit 263s -l str, --list-file str 263s a file containing sequence or read names, one name per 263s line 263s --reverse-complement output reverse complement sequence 263s --out-fasta output fasta format when extract reads from fastq, 263s default output fastq format 263s -o str, --out-file str 263s output file, default: output to stdout 263s --sequential-read start sequential reading, particularly suitable for 263s extracting large numbers of sequences 263s $ pyfastx --version 263s pyfastx version 2.1.0 263s $ pyfastx index protein.fa 263s $ pyfastx index rna.fa 263s $ pyfastx index test.fa 263s $ pyfastx index test.fq 263s $ pyfastx index test.fa.gz 263s $ pyfastx index test.fq.gz 264s $ pyfastx stat protein.fa 264s fileName seqType seqCounts totalBases GC% avgLen medianLen maxLen minLen N50 L50 264s protein.fa protein 17 2265 - 133.235 80.0 419 23 263 4 264s $ pyfastx split -n 2 protein.fa 264s $ pyfastx fq2fa test.fq -o test.fa 264s $ pyfastx subseq protein.fa UPI0000000011:1-4 264s >UPI0000000011:1-4 264s MVDA 264s $ pyfastx sample -n 1 test.fq.gz -o sample.fq 264s $ pyfastx extract protein.fa UPI0000000011 264s >UPI0000000011 status=active 264s MVDAITVLTAIGITVLMLLMVISGAAMIVKELNPNDIFTMQSLKFNRAVTIFKYIGLFIY 264s IPGTIILYATYVKSLLMKS 264s autopkgtest [12:33:31]: test test-cli: -----------------------] 265s autopkgtest [12:33:32]: test test-cli: - - - - - - - - - - results - - - - - - - - - - 265s test-cli PASS 265s autopkgtest [12:33:32]: @@@@@@@@@@@@@@@@@@@@ summary 265s run-unit-test FAIL non-zero exit status 1 265s test-cli PASS 277s nova [W] Using flock in prodstack6-s390x 277s Creating nova instance adt-plucky-s390x-pyfastx-20241113-122906-juju-7f2275-prod-proposed-migration-environment-20-e0234dd7-cf0e-441e-8295-2283d85365a2 from image adt/ubuntu-plucky-s390x-server-20241113.img (UUID e740277e-1f72-40ae-bfbe-46030537c71c)... 277s nova [W] Using flock in prodstack6-s390x 277s Creating nova instance adt-plucky-s390x-pyfastx-20241113-122906-juju-7f2275-prod-proposed-migration-environment-20-e0234dd7-cf0e-441e-8295-2283d85365a2 from image adt/ubuntu-plucky-s390x-server-20241113.img (UUID e740277e-1f72-40ae-bfbe-46030537c71c)...