0s autopkgtest [10:35:12]: starting date and time: 2024-11-13 10:35:12+0000 0s autopkgtest [10:35:12]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [10:35:12]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.c2_d6h2q/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-2@lcy02-71.secgroup --name adt-plucky-amd64-pyfastx-20241113-103511-juju-7f2275-prod-proposed-migration-environment-2-1d4565b4-4d86-4ede-8a8a-788c4dcbdcfa --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 73s autopkgtest [10:36:25]: testbed dpkg architecture: amd64 73s autopkgtest [10:36:25]: testbed apt version: 2.9.8 73s autopkgtest [10:36:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 73s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 73s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 73s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 73s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 73s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 73s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 73s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 73s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 73s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 73s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [639 kB] 73s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 73s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 74s Fetched 2175 kB in 0s (5926 kB/s) 74s Reading package lists... 75s Reading package lists... 76s Building dependency tree... 76s Reading state information... 76s Calculating upgrade... 76s The following NEW packages will be installed: 76s python3.13-gdbm 76s The following packages will be upgraded: 76s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 76s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 76s Need to get 253 kB of archives. 76s After this operation, 147 kB of additional disk space will be used. 76s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 76s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 76s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 76s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 76s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 76s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 76s Fetched 253 kB in 0s (8377 kB/s) 77s (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 ... 75541 files and directories currently installed.) 77s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 77s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 77s Setting up python3-minimal (3.12.7-1) ... 77s (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 ... 75541 files and directories currently installed.) 77s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 77s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 77s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 77s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 77s Selecting previously unselected package python3.13-gdbm. 77s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 77s Unpacking python3.13-gdbm (3.13.0-2) ... 77s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 77s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 77s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 77s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 77s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 77s Setting up python3.13-gdbm (3.13.0-2) ... 77s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 77s Setting up python3 (3.12.7-1) ... 77s Setting up python3-gdbm:amd64 (3.12.7-1) ... 77s Processing triggers for man-db (2.12.1-3) ... 78s Processing triggers for libc-bin (2.40-1ubuntu3) ... 78s Reading package lists... 78s Building dependency tree... 78s Reading state information... 79s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 79s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 79s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 79s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 80s Reading package lists... 80s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s Calculating upgrade... 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s autopkgtest [10:36:35]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 84s autopkgtest [10:36:36]: @@@@@@@@@@@@@@@@@@@@ apt-source pyfastx 85s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (dsc) [2289 B] 85s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (tar) [230 kB] 85s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (diff) [7412 B] 85s gpgv: Signature made Fri Aug 30 18:49:12 2024 UTC 85s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 85s gpgv: issuer "emollier@debian.org" 85s gpgv: Can't check signature: No public key 85s dpkg-source: warning: cannot verify inline signature for ./pyfastx_2.1.0-2.dsc: no acceptable signature found 85s autopkgtest [10:36:37]: testing package pyfastx version 2.1.0-2 85s autopkgtest [10:36:37]: build not needed 85s autopkgtest [10:36:37]: test run-unit-test: preparing testbed 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 86s Starting pkgProblemResolver with broken count: 0 86s Starting 2 pkgProblemResolver with broken count: 0 86s Done 87s The following additional packages will be installed: 87s libpython3.13-minimal libpython3.13-stdlib pyfastx python3-all 87s python3-importlib-metadata python3-packaging python3-pyfaidx python3-pyfastx 87s python3.13 python3.13-minimal 87s Suggested packages: 87s python3.13-venv python3.13-doc binfmt-support 87s Recommended packages: 87s python3-biopython 87s The following NEW packages will be installed: 87s autopkgtest-satdep libpython3.13-minimal libpython3.13-stdlib pyfastx 87s python3-all python3-importlib-metadata python3-packaging python3-pyfaidx 87s python3-pyfastx python3.13 python3.13-minimal 87s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 87s Need to get 6164 kB/6164 kB of archives. 87s After this operation, 23.2 MB of additional disk space will be used. 87s Get:1 /tmp/autopkgtest.HA6zSa/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B] 87s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 87s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 87s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 87s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-metadata all 8.5.0-1 [20.7 kB] 87s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 87s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 87s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfastx amd64 2.1.0-2 [56.7 kB] 87s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 pyfastx amd64 2.1.0-2 [122 kB] 87s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 87s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 87s Fetched 6164 kB in 0s (22.4 MB/s) 87s Selecting previously unselected package libpython3.13-minimal:amd64. 88s (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 ... 75548 files and directories currently installed.) 88s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ... 88s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 88s Selecting previously unselected package python3.13-minimal. 88s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ... 88s Unpacking python3.13-minimal (3.13.0-2) ... 88s Selecting previously unselected package libpython3.13-stdlib:amd64. 88s Preparing to unpack .../02-libpython3.13-stdlib_3.13.0-2_amd64.deb ... 88s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ... 88s Selecting previously unselected package python3-importlib-metadata. 88s Preparing to unpack .../03-python3-importlib-metadata_8.5.0-1_all.deb ... 88s Unpacking python3-importlib-metadata (8.5.0-1) ... 88s Selecting previously unselected package python3-packaging. 88s Preparing to unpack .../04-python3-packaging_24.1-1_all.deb ... 88s Unpacking python3-packaging (24.1-1) ... 88s Selecting previously unselected package python3-pyfaidx. 88s Preparing to unpack .../05-python3-pyfaidx_0.8.1.3-1_all.deb ... 88s Unpacking python3-pyfaidx (0.8.1.3-1) ... 88s Selecting previously unselected package python3-pyfastx. 88s Preparing to unpack .../06-python3-pyfastx_2.1.0-2_amd64.deb ... 88s Unpacking python3-pyfastx (2.1.0-2) ... 88s Selecting previously unselected package pyfastx. 88s Preparing to unpack .../07-pyfastx_2.1.0-2_amd64.deb ... 88s Unpacking pyfastx (2.1.0-2) ... 88s Selecting previously unselected package python3.13. 88s Preparing to unpack .../08-python3.13_3.13.0-2_amd64.deb ... 88s Unpacking python3.13 (3.13.0-2) ... 88s Selecting previously unselected package python3-all. 88s Preparing to unpack .../09-python3-all_3.12.7-1_amd64.deb ... 88s Unpacking python3-all (3.12.7-1) ... 88s Selecting previously unselected package autopkgtest-satdep. 88s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 88s Unpacking autopkgtest-satdep (0) ... 88s Setting up python3-importlib-metadata (8.5.0-1) ... 88s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 88s Setting up python3-packaging (24.1-1) ... 88s Setting up python3.13-minimal (3.13.0-2) ... 89s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 89s Setting up python3-pyfaidx (0.8.1.3-1) ... 89s Setting up python3.13 (3.13.0-2) ... 90s Setting up python3-pyfastx (2.1.0-2) ... 90s Setting up python3-all (3.12.7-1) ... 90s Setting up pyfastx (2.1.0-2) ... 90s Setting up autopkgtest-satdep (0) ... 90s Processing triggers for man-db (2.12.1-3) ... 91s Processing triggers for systemd (256.5-2ubuntu4) ... 93s (Reading database ... 76380 files and directories currently installed.) 93s Removing autopkgtest-satdep (0) ... 93s autopkgtest [10:36:45]: test run-unit-test: [----------------------- 93s tests.test_fakeys (unittest.loader._FailedTest.tests.test_fakeys) ... ERROR 93s tests.test_fasta (unittest.loader._FailedTest.tests.test_fasta) ... ERROR 93s tests.test_fastq (unittest.loader._FailedTest.tests.test_fastq) ... ERROR 93s tests.test_fastx (unittest.loader._FailedTest.tests.test_fastx) ... ERROR 93s tests.test_fqkeys (unittest.loader._FailedTest.tests.test_fqkeys) ... ERROR 93s tests.test_read (unittest.loader._FailedTest.tests.test_read) ... ERROR 93s tests.test_sequence (unittest.loader._FailedTest.tests.test_sequence) ... ERROR 93s tests.test_sequence_error (unittest.loader._FailedTest.tests.test_sequence_error) ... ERROR 93s 93s ====================================================================== 93s ERROR: tests.test_fakeys (unittest.loader._FailedTest.tests.test_fakeys) 93s ---------------------------------------------------------------------- 93s ImportError: Failed to import test module: tests.test_fakeys 93s Traceback (most recent call last): 93s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 93s module = self._get_module_from_name(name) 93s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 93s __import__(name) 93s ~~~~~~~~~~^^^^^^ 93s File "/tmp/autopkgtest.HA6zSa/build.CM0/src/tests/test_fakeys.py", line 3, in 93s import pyfastx 93s ModuleNotFoundError: No module named 'pyfastx' 93s 93s 93s ====================================================================== 93s ERROR: tests.test_fasta (unittest.loader._FailedTest.tests.test_fasta) 93s ---------------------------------------------------------------------- 93s ImportError: Failed to import test module: tests.test_fasta 93s Traceback (most recent call last): 93s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 93s module = self._get_module_from_name(name) 93s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 93s __import__(name) 93s ~~~~~~~~~~^^^^^^ 93s File "/tmp/autopkgtest.HA6zSa/build.CM0/src/tests/test_fasta.py", line 3, in 93s import pyfastx 93s ModuleNotFoundError: No module named 'pyfastx' 93s 93s 93s ====================================================================== 93s ERROR: tests.test_fastq (unittest.loader._FailedTest.tests.test_fastq) 93s ---------------------------------------------------------------------- 93s ImportError: Failed to import test module: tests.test_fastq 93s Traceback (most recent call last): 93s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 93s module = self._get_module_from_name(name) 93s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 93s __import__(name) 93s ~~~~~~~~~~^^^^^^ 93s File "/tmp/autopkgtest.HA6zSa/build.CM0/src/tests/test_fastq.py", line 3, in 93s import pyfastx 93s ModuleNotFoundError: No module named 'pyfastx' 93s 93s 93s ====================================================================== 93s ERROR: tests.test_fastx (unittest.loader._FailedTest.tests.test_fastx) 93s ---------------------------------------------------------------------- 93s ImportError: Failed to import test module: tests.test_fastx 93s Traceback (most recent call last): 93s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 93s module = self._get_module_from_name(name) 93s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 93s __import__(name) 93s ~~~~~~~~~~^^^^^^ 93s File "/tmp/autopkgtest.HA6zSa/build.CM0/src/tests/test_fastx.py", line 3, in 93s import pyfastx 93s ModuleNotFoundError: No module named 'pyfastx' 93s 93s 93s ====================================================================== 93s ERROR: tests.test_fqkeys (unittest.loader._FailedTest.tests.test_fqkeys) 93s ---------------------------------------------------------------------- 93s ImportError: Failed to import test module: tests.test_fqkeys 93s Traceback (most recent call last): 93s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 93s module = self._get_module_from_name(name) 93s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 93s __import__(name) 93s ~~~~~~~~~~^^^^^^ 93s File "/tmp/autopkgtest.HA6zSa/build.CM0/src/tests/test_fqkeys.py", line 3, in 93s import pyfastx 93s ModuleNotFoundError: No module named 'pyfastx' 93s 93s 93s ====================================================================== 93s ERROR: tests.test_read (unittest.loader._FailedTest.tests.test_read) 93s ---------------------------------------------------------------------- 93s ImportError: Failed to import test module: tests.test_read 93s Traceback (most recent call last): 93s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 93s module = self._get_module_from_name(name) 93s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 93s __import__(name) 93s ~~~~~~~~~~^^^^^^ 93s File "/tmp/autopkgtest.HA6zSa/build.CM0/src/tests/test_read.py", line 4, in 93s import pyfastx 93s ModuleNotFoundError: No module named 'pyfastx' 93s 93s 93s ====================================================================== 93s ERROR: tests.test_sequence (unittest.loader._FailedTest.tests.test_sequence) 93s ---------------------------------------------------------------------- 93s ImportError: Failed to import test module: tests.test_sequence 93s Traceback (most recent call last): 93s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 93s module = self._get_module_from_name(name) 93s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 93s __import__(name) 93s ~~~~~~~~~~^^^^^^ 93s File "/tmp/autopkgtest.HA6zSa/build.CM0/src/tests/test_sequence.py", line 3, in 93s import pyfastx 93s ModuleNotFoundError: No module named 'pyfastx' 93s 93s 93s ====================================================================== 93s ERROR: tests.test_sequence_error (unittest.loader._FailedTest.tests.test_sequence_error) 93s ---------------------------------------------------------------------- 93s ImportError: Failed to import test module: tests.test_sequence_error 93s Traceback (most recent call last): 93s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 93s module = self._get_module_from_name(name) 93s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 93s __import__(name) 93s ~~~~~~~~~~^^^^^^ 93s File "/tmp/autopkgtest.HA6zSa/build.CM0/src/tests/test_sequence_error.py", line 3, in 93s import pyfastx 93s ModuleNotFoundError: No module named 'pyfastx' 93s 93s 93s ---------------------------------------------------------------------- 93s Ran 8 tests in 0.001s 93s 93s FAILED (errors=8) 94s autopkgtest [10:36:46]: test run-unit-test: -----------------------] 94s autopkgtest [10:36:46]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 94s run-unit-test FAIL non-zero exit status 1 94s autopkgtest [10:36:46]: test test-cli: preparing testbed 185s autopkgtest [10:38:17]: testbed dpkg architecture: amd64 185s autopkgtest [10:38:17]: testbed apt version: 2.9.8 185s autopkgtest [10:38:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup 186s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 186s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 186s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 186s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 186s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 186s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 186s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 186s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 186s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 186s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [639 kB] 186s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 186s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 186s Fetched 2175 kB in 0s (6475 kB/s) 186s Reading package lists... 188s Reading package lists... 188s Building dependency tree... 188s Reading state information... 188s Calculating upgrade... 189s The following NEW packages will be installed: 189s python3.13-gdbm 189s The following packages will be upgraded: 189s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 189s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 189s Need to get 253 kB of archives. 189s After this operation, 147 kB of additional disk space will be used. 189s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 189s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 189s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 189s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 189s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 189s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 189s Fetched 253 kB in 0s (4432 kB/s) 190s (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 ... 75541 files and directories currently installed.) 190s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 190s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 190s Setting up python3-minimal (3.12.7-1) ... 190s (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 ... 75541 files and directories currently installed.) 190s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 190s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 190s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 190s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 190s Selecting previously unselected package python3.13-gdbm. 190s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 190s Unpacking python3.13-gdbm (3.13.0-2) ... 190s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 190s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 190s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 190s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 190s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 190s Setting up python3.13-gdbm (3.13.0-2) ... 190s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 190s Setting up python3 (3.12.7-1) ... 191s Setting up python3-gdbm:amd64 (3.12.7-1) ... 191s Processing triggers for man-db (2.12.1-3) ... 191s Processing triggers for libc-bin (2.40-1ubuntu3) ... 192s Reading package lists... 192s Building dependency tree... 192s Reading state information... 193s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 193s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 193s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 193s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 193s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 194s Reading package lists... 194s Reading package lists... 195s Building dependency tree... 195s Reading state information... 195s Calculating upgrade... 195s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 195s Reading package lists... 196s Building dependency tree... 196s Reading state information... 196s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 198s Reading package lists... 198s Building dependency tree... 198s Reading state information... 199s Starting pkgProblemResolver with broken count: 0 199s Starting 2 pkgProblemResolver with broken count: 0 199s Done 200s The following additional packages will be installed: 200s pyfastx python3-importlib-metadata python3-packaging python3-pyfaidx 200s python3-pyfastx 200s Recommended packages: 200s python3-biopython 200s The following NEW packages will be installed: 200s autopkgtest-satdep pyfastx python3-importlib-metadata python3-packaging 200s python3-pyfaidx python3-pyfastx 200s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 200s Need to get 270 kB/271 kB of archives. 200s After this operation, 751 kB of additional disk space will be used. 200s Get:1 /tmp/autopkgtest.HA6zSa/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 200s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-metadata all 8.5.0-1 [20.7 kB] 200s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 200s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 200s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfastx amd64 2.1.0-2 [56.7 kB] 200s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 pyfastx amd64 2.1.0-2 [122 kB] 200s Fetched 270 kB in 0s (3409 kB/s) 200s Selecting previously unselected package python3-importlib-metadata. 200s (Reading database ... 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Removing autopkgtest-satdep (0) ... 205s autopkgtest [10:38:37]: test test-cli: [----------------------- 205s $ pyfastx --help 206s usage: pyfastx COMMAND [OPTIONS] 206s 206s A command line tool for FASTA/Q file manipulation 206s 206s options: 206s -h, --help show this help message and exit 206s -v, --version show program's version number and exit 206s 206s Commands: 206s 206s index build index for fasta/q file 206s stat show detailed statistics information of fasta/q file 206s split split fasta/q file into multiple files 206s fq2fa convert fastq file to fasta file 206s subseq get subsequences from fasta file by region 206s sample randomly sample sequences from fasta or fastq file 206s extract extract full sequences or reads from fasta/q file 206s $ # Found pyfastx commands: 'index stat split fq2fa subseq sample extract' 206s $ pyfastx index --help 206s usage: pyfastx index [-h] [-f] fastx [fastx ...] 206s 206s positional arguments: 206s fastx fasta or fastq file, gzip support 206s 206s options: 206s -h, --help show this help message and exit 206s -f, --full build full index, base composition will be calculated 206s $ pyfastx stat --help 206s usage: pyfastx stat [-h] fastx [fastx ...] 206s 206s positional arguments: 206s fastx fasta or fastq file, gzip support 206s 206s options: 206s -h, --help show this help message and exit 206s $ pyfastx split --help 206s usage: pyfastx split [-h] (-n int | -c int) [-o str] fastx 206s 206s positional arguments: 206s fastx fasta or fastq file, gzip support 206s 206s options: 206s -h, --help show this help message and exit 206s -n int split a fasta/q file into N new files with even size 206s -c int split a fasta/q file into multiple files containing 206s the same sequence counts 206s -o str, --out-dir str 206s output directory, default is current folder 206s $ pyfastx fq2fa --help 206s usage: pyfastx fq2fa [-h] [-o str] fastx 206s 206s positional arguments: 206s fastx fastq file, gzip support 206s 206s options: 206s -h, --help show this help message and exit 206s -o str, --out-file str 206s output file, default: output to stdout 206s $ pyfastx subseq --help 206s usage: pyfastx subseq [-h] [-r str | -b str] [-o str] fastx [region ...] 206s 206s positional arguments: 206s fastx input fasta file, gzip support 206s region format is chr:start-end, start and end position is 206s 1-based, multiple regions were separated by space 206s 206s options: 206s -h, --help show this help message and exit 206s -r str, --region-file str 206s tab-delimited file, one region per line, both start 206s and end position are 1-based 206s -b str, --bed-file str 206s tab-delimited BED file, 0-based start position and 206s 1-based end position 206s -o str, --out-file str 206s output file, default: output to stdout 206s $ pyfastx sample --help 206s usage: pyfastx sample [-h] (-n int | -p float) [-s int] [--sequential-read] 206s [-o str] 206s fastx 206s 206s positional arguments: 206s fastx fasta or fastq file, gzip support 206s 206s options: 206s -h, --help show this help message and exit 206s -n int number of sequences to be sampled 206s -p float proportion of sequences to be sampled, 0~1 206s -s int, --seed int random seed, default is the current system time 206s --sequential-read start sequential reading, particularly suitable for 206s sampling large numbers of sequences 206s -o str, --out-file str 206s output file, default: output to stdout 206s $ pyfastx extract --help 206s usage: pyfastx extract [-h] [-l str] [--reverse-complement] [--out-fasta] 206s [-o str] [--sequential-read] 206s fastx [name ...] 206s 206s positional arguments: 206s fastx fasta or fastq file, gzip support 206s name sequence name or read name, multiple names were 206s separated by space 206s 206s options: 206s -h, --help show this help message and exit 206s -l str, --list-file str 206s a file containing sequence or read names, one name per 206s line 206s --reverse-complement output reverse complement sequence 206s --out-fasta output fasta format when extract reads from fastq, 206s default output fastq format 206s -o str, --out-file str 206s output file, default: output to stdout 206s --sequential-read start sequential reading, particularly suitable for 206s extracting large numbers of sequences 206s $ pyfastx --version 207s pyfastx version 2.1.0 207s $ pyfastx index protein.fa 207s $ pyfastx index rna.fa 207s $ pyfastx index test.fa 207s $ pyfastx index test.fq 207s $ pyfastx index test.fa.gz 207s $ pyfastx index test.fq.gz 207s $ pyfastx stat protein.fa 207s fileName seqType seqCounts totalBases GC% avgLen medianLen maxLen minLen N50 L50 207s protein.fa protein 17 2265 - 133.235 80.0 419 23 263 4 208s $ pyfastx split -n 2 protein.fa 208s $ pyfastx fq2fa test.fq -o test.fa 208s $ pyfastx subseq protein.fa UPI0000000011:1-4 208s >UPI0000000011:1-4 208s MVDA 208s $ pyfastx sample -n 1 test.fq.gz -o sample.fq 208s $ pyfastx extract protein.fa UPI0000000011 208s >UPI0000000011 status=active 208s MVDAITVLTAIGITVLMLLMVISGAAMIVKELNPNDIFTMQSLKFNRAVTIFKYIGLFIY 208s IPGTIILYATYVKSLLMKS 209s autopkgtest [10:38:41]: test test-cli: -----------------------] 209s test-cli PASS 209s autopkgtest [10:38:41]: test test-cli: - - - - - - - - - - results - - - - - - - - - - 209s autopkgtest [10:38:41]: @@@@@@@@@@@@@@@@@@@@ summary 209s run-unit-test FAIL non-zero exit status 1 209s test-cli PASS 226s virt: nova [W] Skipping flock for amd64 226s virt: Creating nova instance adt-plucky-amd64-pyfastx-20241113-103511-juju-7f2275-prod-proposed-migration-environment-2-1d4565b4-4d86-4ede-8a8a-788c4dcbdcfa from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 76b850f9-98f4-4b79-af06-fa11000b95b2)... 226s virt: nova [W] Skipping flock for amd64 226s virt: Creating nova instance adt-plucky-amd64-pyfastx-20241113-103511-juju-7f2275-prod-proposed-migration-environment-2-1d4565b4-4d86-4ede-8a8a-788c4dcbdcfa from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 76b850f9-98f4-4b79-af06-fa11000b95b2)...