0s autopkgtest [09:57:54]: starting date and time: 2024-11-13 09:57:54+0000 0s autopkgtest [09:57:54]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [09:57:54]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.d5y2ukta/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-12.secgroup --name adt-plucky-arm64-pyfastx-20241113-095754-juju-7f2275-prod-proposed-migration-environment-20-579ce118-fe53-4275-8fe8-cc2d87ce190b --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 118s autopkgtest [09:59:52]: testbed dpkg architecture: arm64 119s autopkgtest [09:59:53]: testbed apt version: 2.9.8 119s autopkgtest [09:59:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 120s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 120s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 120s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 120s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 120s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 120s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 120s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 120s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 120s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 120s Fetched 1794 kB in 1s (2221 kB/s) 120s Reading package lists... 123s Reading package lists... 124s Building dependency tree... 124s Reading state information... 125s Calculating upgrade... 125s The following NEW packages will be installed: 125s python3.13-gdbm 125s The following packages will be upgraded: 125s libpython3-stdlib python3 python3-gdbm python3-minimal 125s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 125s Need to get 101 kB of archives. 125s After this operation, 141 kB of additional disk space will be used. 125s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 125s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 125s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 125s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 126s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 126s Fetched 101 kB in 0s (290 kB/s) 126s (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 ... 79924 files and directories currently installed.) 126s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 126s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 126s Setting up python3-minimal (3.12.7-1) ... 127s (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 ... 79924 files and directories currently installed.) 127s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 127s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 127s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 127s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 127s Selecting previously unselected package python3.13-gdbm. 127s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 127s Unpacking python3.13-gdbm (3.13.0-2) ... 127s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 127s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 127s Setting up python3.13-gdbm (3.13.0-2) ... 127s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 127s Setting up python3 (3.12.7-1) ... 127s Setting up python3-gdbm:arm64 (3.12.7-1) ... 127s Processing triggers for man-db (2.12.1-3) ... 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 129s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 129s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 129s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 130s Reading package lists... 130s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s Calculating upgrade... 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s autopkgtest [10:00:10]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 136s autopkgtest [10:00:10]: @@@@@@@@@@@@@@@@@@@@ apt-source pyfastx 138s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (dsc) [2289 B] 138s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (tar) [230 kB] 138s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (diff) [7412 B] 138s gpgv: Signature made Fri Aug 30 18:49:12 2024 UTC 138s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 138s gpgv: issuer "emollier@debian.org" 138s gpgv: Can't check signature: No public key 138s dpkg-source: warning: cannot verify inline signature for ./pyfastx_2.1.0-2.dsc: no acceptable signature found 138s autopkgtest [10:00:12]: testing package pyfastx version 2.1.0-2 139s autopkgtest [10:00:13]: build not needed 139s autopkgtest [10:00:13]: test run-unit-test: preparing testbed 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 142s Starting pkgProblemResolver with broken count: 0 142s Starting 2 pkgProblemResolver with broken count: 0 142s Done 143s The following additional packages will be installed: 143s libpython3.13-minimal libpython3.13-stdlib pyfastx python3-all 143s python3-importlib-metadata python3-packaging python3-pyfaidx python3-pyfastx 143s python3.13 python3.13-minimal 143s Suggested packages: 143s python3.13-venv python3.13-doc binfmt-support 143s Recommended packages: 143s python3-biopython 143s The following NEW packages will be installed: 143s autopkgtest-satdep libpython3.13-minimal libpython3.13-stdlib pyfastx 143s python3-all python3-importlib-metadata python3-packaging python3-pyfaidx 143s python3-pyfastx python3.13 python3.13-minimal 143s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 143s Need to get 6040 kB/6040 kB of archives. 143s After this operation, 24.9 MB of additional disk space will be used. 143s Get:1 /tmp/autopkgtest.VT0k44/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 143s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 143s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 143s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 144s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-importlib-metadata all 8.5.0-1 [20.7 kB] 144s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 144s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 144s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyfastx arm64 2.1.0-2 [56.1 kB] 144s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 pyfastx arm64 2.1.0-2 [122 kB] 144s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 144s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 144s Fetched 6040 kB in 1s (4659 kB/s) 144s Selecting previously unselected package libpython3.13-minimal:arm64. 144s (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 ... 79931 files and directories currently installed.) 144s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ... 144s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 145s Selecting previously unselected package python3.13-minimal. 145s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ... 145s Unpacking python3.13-minimal (3.13.0-2) ... 145s Selecting previously unselected package libpython3.13-stdlib:arm64. 145s Preparing to unpack .../02-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 145s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 145s Selecting previously unselected package python3-importlib-metadata. 145s Preparing to unpack .../03-python3-importlib-metadata_8.5.0-1_all.deb ... 145s Unpacking python3-importlib-metadata (8.5.0-1) ... 145s Selecting previously unselected package python3-packaging. 145s Preparing to unpack .../04-python3-packaging_24.1-1_all.deb ... 145s Unpacking python3-packaging (24.1-1) ... 145s Selecting previously unselected package python3-pyfaidx. 145s Preparing to unpack .../05-python3-pyfaidx_0.8.1.3-1_all.deb ... 145s Unpacking python3-pyfaidx (0.8.1.3-1) ... 145s Selecting previously unselected package python3-pyfastx. 145s Preparing to unpack .../06-python3-pyfastx_2.1.0-2_arm64.deb ... 145s Unpacking python3-pyfastx (2.1.0-2) ... 145s Selecting previously unselected package pyfastx. 145s Preparing to unpack .../07-pyfastx_2.1.0-2_arm64.deb ... 145s Unpacking pyfastx (2.1.0-2) ... 145s Selecting previously unselected package python3.13. 145s Preparing to unpack .../08-python3.13_3.13.0-2_arm64.deb ... 145s Unpacking python3.13 (3.13.0-2) ... 145s Selecting previously unselected package python3-all. 145s Preparing to unpack .../09-python3-all_3.12.7-1_arm64.deb ... 145s Unpacking python3-all (3.12.7-1) ... 145s Selecting previously unselected package autopkgtest-satdep. 145s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 145s Unpacking autopkgtest-satdep (0) ... 145s Setting up python3-importlib-metadata (8.5.0-1) ... 145s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 145s Setting up python3-packaging (24.1-1) ... 146s Setting up python3.13-minimal (3.13.0-2) ... 147s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... 147s Setting up python3-pyfaidx (0.8.1.3-1) ... 147s Setting up python3.13 (3.13.0-2) ... 148s Setting up python3-pyfastx (2.1.0-2) ... 148s Setting up python3-all (3.12.7-1) ... 148s Setting up pyfastx (2.1.0-2) ... 148s Setting up autopkgtest-satdep (0) ... 148s Processing triggers for man-db (2.12.1-3) ... 148s Processing triggers for systemd (256.5-2ubuntu4) ... 154s (Reading database ... 80763 files and directories currently installed.) 154s Removing autopkgtest-satdep (0) ... 155s autopkgtest [10:00:29]: test run-unit-test: [----------------------- 155s tests.test_fakeys (unittest.loader._FailedTest.tests.test_fakeys) ... ERROR 155s tests.test_fasta (unittest.loader._FailedTest.tests.test_fasta) ... ERROR 155s tests.test_fastq (unittest.loader._FailedTest.tests.test_fastq) ... ERROR 155s tests.test_fastx (unittest.loader._FailedTest.tests.test_fastx) ... ERROR 155s tests.test_fqkeys (unittest.loader._FailedTest.tests.test_fqkeys) ... ERROR 155s tests.test_read (unittest.loader._FailedTest.tests.test_read) ... ERROR 155s tests.test_sequence (unittest.loader._FailedTest.tests.test_sequence) ... ERROR 155s tests.test_sequence_error (unittest.loader._FailedTest.tests.test_sequence_error) ... ERROR 155s 155s ====================================================================== 155s ERROR: tests.test_fakeys (unittest.loader._FailedTest.tests.test_fakeys) 155s ---------------------------------------------------------------------- 155s ImportError: Failed to import test module: tests.test_fakeys 155s Traceback (most recent call last): 155s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 155s module = self._get_module_from_name(name) 155s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 155s __import__(name) 155s ~~~~~~~~~~^^^^^^ 155s File "/tmp/autopkgtest.VT0k44/build.cQG/src/tests/test_fakeys.py", line 3, in 155s import pyfastx 155s ModuleNotFoundError: No module named 'pyfastx' 155s 155s 155s ====================================================================== 155s ERROR: tests.test_fasta (unittest.loader._FailedTest.tests.test_fasta) 155s ---------------------------------------------------------------------- 155s ImportError: Failed to import test module: tests.test_fasta 155s Traceback (most recent call last): 155s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 155s module = self._get_module_from_name(name) 155s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 155s __import__(name) 155s ~~~~~~~~~~^^^^^^ 155s File "/tmp/autopkgtest.VT0k44/build.cQG/src/tests/test_fasta.py", line 3, in 155s import pyfastx 155s ModuleNotFoundError: No module named 'pyfastx' 155s 155s 155s ====================================================================== 155s ERROR: tests.test_fastq (unittest.loader._FailedTest.tests.test_fastq) 155s ---------------------------------------------------------------------- 155s ImportError: Failed to import test module: tests.test_fastq 155s Traceback (most recent call last): 155s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 155s module = self._get_module_from_name(name) 155s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 155s __import__(name) 155s ~~~~~~~~~~^^^^^^ 155s File "/tmp/autopkgtest.VT0k44/build.cQG/src/tests/test_fastq.py", line 3, in 155s import pyfastx 155s ModuleNotFoundError: No module named 'pyfastx' 155s 155s 155s ====================================================================== 155s ERROR: tests.test_fastx (unittest.loader._FailedTest.tests.test_fastx) 155s ---------------------------------------------------------------------- 155s ImportError: Failed to import test module: tests.test_fastx 155s Traceback (most recent call last): 155s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 155s module = self._get_module_from_name(name) 155s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 155s __import__(name) 155s ~~~~~~~~~~^^^^^^ 155s File "/tmp/autopkgtest.VT0k44/build.cQG/src/tests/test_fastx.py", line 3, in 155s import pyfastx 155s ModuleNotFoundError: No module named 'pyfastx' 155s 155s 155s ====================================================================== 155s ERROR: tests.test_fqkeys (unittest.loader._FailedTest.tests.test_fqkeys) 155s ---------------------------------------------------------------------- 155s ImportError: Failed to import test module: tests.test_fqkeys 155s Traceback (most recent call last): 155s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 155s module = self._get_module_from_name(name) 155s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 155s __import__(name) 155s ~~~~~~~~~~^^^^^^ 155s File "/tmp/autopkgtest.VT0k44/build.cQG/src/tests/test_fqkeys.py", line 3, in 155s import pyfastx 155s ModuleNotFoundError: No module named 'pyfastx' 155s 155s 155s ====================================================================== 155s ERROR: tests.test_read (unittest.loader._FailedTest.tests.test_read) 155s ---------------------------------------------------------------------- 155s ImportError: Failed to import test module: tests.test_read 155s Traceback (most recent call last): 155s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 155s module = self._get_module_from_name(name) 155s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 155s __import__(name) 155s ~~~~~~~~~~^^^^^^ 155s File "/tmp/autopkgtest.VT0k44/build.cQG/src/tests/test_read.py", line 4, in 155s import pyfastx 155s ModuleNotFoundError: No module named 'pyfastx' 155s 155s 155s ====================================================================== 155s ERROR: tests.test_sequence (unittest.loader._FailedTest.tests.test_sequence) 155s ---------------------------------------------------------------------- 155s ImportError: Failed to import test module: tests.test_sequence 155s Traceback (most recent call last): 155s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 155s module = self._get_module_from_name(name) 155s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 155s __import__(name) 155s ~~~~~~~~~~^^^^^^ 155s File "/tmp/autopkgtest.VT0k44/build.cQG/src/tests/test_sequence.py", line 3, in 155s import pyfastx 155s ModuleNotFoundError: No module named 'pyfastx' 155s 155s 155s ====================================================================== 155s ERROR: tests.test_sequence_error (unittest.loader._FailedTest.tests.test_sequence_error) 155s ---------------------------------------------------------------------- 155s ImportError: Failed to import test module: tests.test_sequence_error 155s Traceback (most recent call last): 155s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 155s module = self._get_module_from_name(name) 155s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 155s __import__(name) 155s ~~~~~~~~~~^^^^^^ 155s File "/tmp/autopkgtest.VT0k44/build.cQG/src/tests/test_sequence_error.py", line 3, in 155s import pyfastx 155s ModuleNotFoundError: No module named 'pyfastx' 155s 155s 155s ---------------------------------------------------------------------- 155s Ran 8 tests in 0.002s 155s 155s FAILED (errors=8) 156s autopkgtest [10:00:30]: test run-unit-test: -----------------------] 156s run-unit-test FAIL non-zero exit status 1 156s autopkgtest [10:00:30]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 157s autopkgtest [10:00:31]: test test-cli: preparing testbed 291s autopkgtest [10:02:45]: testbed dpkg architecture: arm64 291s autopkgtest [10:02:45]: testbed apt version: 2.9.8 291s autopkgtest [10:02:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 292s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 293s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 293s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 293s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 293s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 293s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 293s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 293s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 293s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 293s Fetched 1794 kB in 1s (1566 kB/s) 293s Reading package lists... 296s Reading package lists... 296s Building dependency tree... 296s Reading state information... 297s Calculating upgrade... 298s The following NEW packages will be installed: 298s python3.13-gdbm 298s The following packages will be upgraded: 298s libpython3-stdlib python3 python3-gdbm python3-minimal 298s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 298s Need to get 101 kB of archives. 298s After this operation, 141 kB of additional disk space will be used. 298s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 298s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 298s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 298s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 298s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 299s Fetched 101 kB in 0s (268 kB/s) 299s (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 ... 79924 files and directories currently installed.) 299s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 299s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 299s Setting up python3-minimal (3.12.7-1) ... 299s (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 ... 79924 files and directories currently installed.) 299s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 300s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 300s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 300s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 300s Selecting previously unselected package python3.13-gdbm. 300s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 300s Unpacking python3.13-gdbm (3.13.0-2) ... 300s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 300s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 300s Setting up python3.13-gdbm (3.13.0-2) ... 300s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 300s Setting up python3 (3.12.7-1) ... 300s Setting up python3-gdbm:arm64 (3.12.7-1) ... 300s Processing triggers for man-db (2.12.1-3) ... 301s Reading package lists... 301s Building dependency tree... 301s Reading state information... 302s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 302s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 303s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 303s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 303s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 304s Reading package lists... 304s Reading package lists... 304s Building dependency tree... 304s Reading state information... 305s Calculating upgrade... 305s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 305s Reading package lists... 305s Building dependency tree... 305s Reading state information... 306s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 311s Reading package lists... 311s Building dependency tree... 311s Reading state information... 312s Starting pkgProblemResolver with broken count: 0 312s Starting 2 pkgProblemResolver with broken count: 0 312s Done 312s The following additional packages will be installed: 312s pyfastx python3-importlib-metadata python3-packaging python3-pyfaidx 312s python3-pyfastx 312s Recommended packages: 312s python3-biopython 313s The following NEW packages will be installed: 313s autopkgtest-satdep pyfastx python3-importlib-metadata python3-packaging 313s python3-pyfaidx python3-pyfastx 313s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 313s Need to get 269 kB/270 kB of archives. 313s After this operation, 762 kB of additional disk space will be used. 313s Get:1 /tmp/autopkgtest.VT0k44/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 313s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-importlib-metadata all 8.5.0-1 [20.7 kB] 313s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 313s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 313s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyfastx arm64 2.1.0-2 [56.1 kB] 313s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 pyfastx arm64 2.1.0-2 [122 kB] 313s Fetched 269 kB in 1s (528 kB/s) 313s Selecting previously unselected package python3-importlib-metadata. 314s (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 ... 79931 files and directories currently installed.) 314s Preparing to unpack .../0-python3-importlib-metadata_8.5.0-1_all.deb ... 314s Unpacking python3-importlib-metadata (8.5.0-1) ... 314s Selecting previously unselected package python3-packaging. 314s Preparing to unpack .../1-python3-packaging_24.1-1_all.deb ... 314s Unpacking python3-packaging (24.1-1) ... 314s Selecting previously unselected package python3-pyfaidx. 314s Preparing to unpack .../2-python3-pyfaidx_0.8.1.3-1_all.deb ... 314s Unpacking python3-pyfaidx (0.8.1.3-1) ... 314s Selecting previously unselected package python3-pyfastx. 314s Preparing to unpack .../3-python3-pyfastx_2.1.0-2_arm64.deb ... 314s Unpacking python3-pyfastx (2.1.0-2) ... 314s Selecting previously unselected package pyfastx. 314s Preparing to unpack .../4-pyfastx_2.1.0-2_arm64.deb ... 314s Unpacking pyfastx (2.1.0-2) ... 314s Selecting previously unselected package autopkgtest-satdep. 314s Preparing to unpack .../5-2-autopkgtest-satdep.deb ... 314s Unpacking autopkgtest-satdep (0) ... 314s Setting up python3-importlib-metadata (8.5.0-1) ... 314s Setting up python3-packaging (24.1-1) ... 314s Setting up python3-pyfaidx (0.8.1.3-1) ... 314s Setting up python3-pyfastx (2.1.0-2) ... 314s Setting up pyfastx (2.1.0-2) ... 314s Setting up autopkgtest-satdep (0) ... 314s Processing triggers for man-db (2.12.1-3) ... 318s (Reading database ... 80028 files and directories currently installed.) 318s Removing autopkgtest-satdep (0) ... 320s autopkgtest [10:03:14]: test test-cli: [----------------------- 320s $ pyfastx --help 320s usage: pyfastx COMMAND [OPTIONS] 320s 320s A command line tool for FASTA/Q file manipulation 320s 320s options: 320s -h, --help show this help message and exit 320s -v, --version show program's version number and exit 320s 320s Commands: 320s 320s index build index for fasta/q file 320s stat show detailed statistics information of fasta/q file 320s split split fasta/q file into multiple files 320s fq2fa convert fastq file to fasta file 320s subseq get subsequences from fasta file by region 320s sample randomly sample sequences from fasta or fastq file 320s extract extract full sequences or reads from fasta/q file 320s $ # Found pyfastx commands: 'index stat split fq2fa subseq sample extract' 320s $ pyfastx index --help 320s usage: pyfastx index [-h] [-f] fastx [fastx ...] 320s 320s positional arguments: 320s fastx fasta or fastq file, gzip support 320s 320s options: 320s -h, --help show this help message and exit 320s -f, --full build full index, base composition will be calculated 320s $ pyfastx stat --help 321s usage: pyfastx stat [-h] fastx [fastx ...] 321s 321s positional arguments: 321s fastx fasta or fastq file, gzip support 321s 321s options: 321s -h, --help show this help message and exit 321s $ pyfastx split --help 321s usage: pyfastx split [-h] (-n int | -c int) [-o str] fastx 321s 321s positional arguments: 321s fastx fasta or fastq file, gzip support 321s 321s options: 321s -h, --help show this help message and exit 321s -n int split a fasta/q file into N new files with even size 321s -c int split a fasta/q file into multiple files containing 321s the same sequence counts 321s -o str, --out-dir str 321s output directory, default is current folder 321s $ pyfastx fq2fa --help 321s usage: pyfastx fq2fa [-h] [-o str] fastx 321s 321s positional arguments: 321s fastx fastq file, gzip support 321s 321s options: 321s -h, --help show this help message and exit 321s -o str, --out-file str 321s output file, default: output to stdout 321s $ pyfastx subseq --help 321s usage: pyfastx subseq [-h] [-r str | -b str] [-o str] fastx [region ...] 321s 321s positional arguments: 321s fastx input fasta file, gzip support 321s region format is chr:start-end, start and end position is 321s 1-based, multiple regions were separated by space 321s 321s options: 321s -h, --help show this help message and exit 321s -r str, --region-file str 321s tab-delimited file, one region per line, both start 321s and end position are 1-based 321s -b str, --bed-file str 321s tab-delimited BED file, 0-based start position and 321s 1-based end position 321s -o str, --out-file str 321s output file, default: output to stdout 321s $ pyfastx sample --help 322s usage: pyfastx sample [-h] (-n int | -p float) [-s int] [--sequential-read] 322s [-o str] 322s fastx 322s 322s positional arguments: 322s fastx fasta or fastq file, gzip support 322s 322s options: 322s -h, --help show this help message and exit 322s -n int number of sequences to be sampled 322s -p float proportion of sequences to be sampled, 0~1 322s -s int, --seed int random seed, default is the current system time 322s --sequential-read start sequential reading, particularly suitable for 322s sampling large numbers of sequences 322s -o str, --out-file str 322s output file, default: output to stdout 322s $ pyfastx extract --help 322s usage: pyfastx extract [-h] [-l str] [--reverse-complement] [--out-fasta] 322s [-o str] [--sequential-read] 322s fastx [name ...] 322s 322s positional arguments: 322s fastx fasta or fastq file, gzip support 322s name sequence name or read name, multiple names were 322s separated by space 322s 322s options: 322s -h, --help show this help message and exit 322s -l str, --list-file str 322s a file containing sequence or read names, one name per 322s line 322s --reverse-complement output reverse complement sequence 322s --out-fasta output fasta format when extract reads from fastq, 322s default output fastq format 322s -o str, --out-file str 322s output file, default: output to stdout 322s --sequential-read start sequential reading, particularly suitable for 322s extracting large numbers of sequences 322s $ pyfastx --version 322s pyfastx version 2.1.0 322s $ pyfastx index protein.fa 323s $ pyfastx index rna.fa 323s $ pyfastx index test.fa 323s $ pyfastx index test.fq 323s $ pyfastx index test.fa.gz 323s $ pyfastx index test.fq.gz 323s $ pyfastx stat protein.fa 324s fileName seqType seqCounts totalBases GC% avgLen medianLen maxLen minLen N50 L50 324s protein.fa protein 17 2265 - 133.235 80.0 419 23 263 4 324s $ pyfastx split -n 2 protein.fa 324s $ pyfastx fq2fa test.fq -o test.fa 324s $ pyfastx subseq protein.fa UPI0000000011:1-4 324s >UPI0000000011:1-4 324s MVDA 324s $ pyfastx sample -n 1 test.fq.gz -o sample.fq 324s $ pyfastx extract protein.fa UPI0000000011 324s >UPI0000000011 status=active 324s MVDAITVLTAIGITVLMLLMVISGAAMIVKELNPNDIFTMQSLKFNRAVTIFKYIGLFIY 324s IPGTIILYATYVKSLLMKS 325s autopkgtest [10:03:19]: test test-cli: -----------------------] 325s test-cli PASS 325s autopkgtest [10:03:19]: test test-cli: - - - - - - - - - - results - - - - - - - - - - 326s autopkgtest [10:03:20]: @@@@@@@@@@@@@@@@@@@@ summary 326s run-unit-test FAIL non-zero exit status 1 326s test-cli PASS 346s nova [W] Skipping flock in bos03-arm64 346s Creating nova instance adt-plucky-arm64-pyfastx-20241113-095754-juju-7f2275-prod-proposed-migration-environment-20-579ce118-fe53-4275-8fe8-cc2d87ce190b from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)... 346s nova [W] Skipping flock in bos03-arm64 346s Creating nova instance adt-plucky-arm64-pyfastx-20241113-095754-juju-7f2275-prod-proposed-migration-environment-20-579ce118-fe53-4275-8fe8-cc2d87ce190b from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...