0s autopkgtest [19:46:16]: starting date and time: 2025-10-20 19:46:16+0000 0s autopkgtest [19:46:16]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [19:46:16]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.s8b1u9c5/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:python-pluggy --apt-upgrade atropos --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.4.2-1 python-pluggy/1.6.0-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-4.secgroup --name adt-resolute-arm64-atropos-20251020-194615-juju-7f2275-prod-proposed-migration-environment-2-357aec6f-9ae6-42c4-b38e-3851166d1a56 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-atropos-20251020-194615-juju-7f2275-prod-proposed-migration-environment-2-357aec6f-9ae6-42c4-b38e-3851166d1a56 from image adt/ubuntu-resolute-arm64-server-20251020.img (UUID 53f7e888-0b33-40b7-be7f-09b2db152d64)... 60s autopkgtest [19:47:16]: testbed dpkg architecture: arm64 60s autopkgtest [19:47:16]: testbed apt version: 3.1.8ubuntu1 61s autopkgtest [19:47:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup 61s autopkgtest [19:47:17]: testbed release detected to be: None 62s autopkgtest [19:47:18]: updating testbed package index (apt update) 62s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 62s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 62s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 63s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 63s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [646 kB] 63s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [59.3 kB] 63s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [14.3 kB] 63s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 63s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [115 kB] 63s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [43.8 kB] 63s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [409 kB] 63s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [5672 B] 63s Fetched 1382 kB in 1s (1390 kB/s) 64s Reading package lists... 65s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 65s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 65s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 65s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 66s Reading package lists... 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s Calculating upgrade... 67s The following packages will be upgraded: 67s libbrotli1 libjson-c5 python3-inflect python3-oauthlib python3-zipp 67s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s Need to get 512 kB of archives. 67s After this operation, 31.7 kB of additional disk space will be used. 67s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libjson-c5 arm64 0.18+ds-1.1 [37.5 kB] 67s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libbrotli1 arm64 1.1.0-2build6 [336 kB] 67s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-inflect all 7.5.0-1 [33.9 kB] 67s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-oauthlib all 3.3.1-1 [93.5 kB] 68s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-zipp all 3.23.0-1 [10.4 kB] 68s dpkg-preconfigure: unable to re-open stdin: No such file or directory 68s Fetched 512 kB in 1s (811 kB/s) 69s (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 ... 83364 files and directories currently installed.) 69s Preparing to unpack .../libjson-c5_0.18+ds-1.1_arm64.deb ... 69s Unpacking libjson-c5:arm64 (0.18+ds-1.1) over (0.18+ds-1) ... 69s Preparing to unpack .../libbrotli1_1.1.0-2build6_arm64.deb ... 69s Unpacking libbrotli1:arm64 (1.1.0-2build6) over (1.1.0-2build5) ... 69s Preparing to unpack .../python3-inflect_7.5.0-1_all.deb ... 69s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 69s Preparing to unpack .../python3-oauthlib_3.3.1-1_all.deb ... 69s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 69s Preparing to unpack .../python3-zipp_3.23.0-1_all.deb ... 69s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 70s Setting up libbrotli1:arm64 (1.1.0-2build6) ... 70s Setting up python3-zipp (3.23.0-1) ... 70s Setting up python3-inflect (7.5.0-1) ... 70s Setting up python3-oauthlib (3.3.1-1) ... 70s Setting up libjson-c5:arm64 (0.18+ds-1.1) ... 70s Processing triggers for libc-bin (2.42-0ubuntu3) ... 70s autopkgtest [19:47:26]: upgrading testbed (apt dist-upgrade and autopurge) 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s Calculating upgrade... 72s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 72s Solving dependencies... 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s autopkgtest [19:47:31]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 76s autopkgtest [19:47:32]: @@@@@@@@@@@@@@@@@@@@ apt-source atropos 78s Get:1 http://ftpmaster.internal/ubuntu resolute/universe atropos 1.1.32+dfsg-2build2 (dsc) [2258 B] 78s Get:2 http://ftpmaster.internal/ubuntu resolute/universe atropos 1.1.32+dfsg-2build2 (tar) [3117 kB] 78s Get:3 http://ftpmaster.internal/ubuntu resolute/universe atropos 1.1.32+dfsg-2build2 (diff) [6900 B] 78s gpgv: Signature made Tue Mar 4 15:39:30 2025 UTC 78s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 78s gpgv: Can't check signature: No public key 78s dpkg-source: warning: cannot verify inline signature for ./atropos_1.1.32+dfsg-2build2.dsc: no acceptable signature found 79s autopkgtest [19:47:35]: testing package atropos version 1.1.32+dfsg-2build2 79s autopkgtest [19:47:35]: build not needed 80s autopkgtest [19:47:36]: test run-unit-test: preparing testbed 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Solving dependencies... 81s The following NEW packages will be installed: 81s atropos libdeflate0 libhts3t64 libhtscodecs2 python3-all python3-iniconfig 81s python3-packaging python3-pluggy python3-pysam python3-pytest 81s 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 81s Need to get 4767 kB of archives. 81s After this operation, 40.4 MB of additional disk space will be used. 81s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 81s Get:2 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 81s Get:3 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 82s Get:4 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pysam arm64 0.23.0+ds-1build1 [3621 kB] 82s Get:5 http://ftpmaster.internal/ubuntu resolute/universe arm64 atropos arm64 1.1.32+dfsg-2build2 [226 kB] 82s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-all arm64 3.13.7-1 [884 B] 82s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 82s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-packaging all 25.0-1 [52.8 kB] 82s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-pluggy all 1.6.0-1 [21.0 kB] 82s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-pytest all 8.4.2-1 [268 kB] 83s Fetched 4767 kB in 1s (3381 kB/s) 83s Selecting previously unselected package libdeflate0:arm64. 83s (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 ... 83374 files and directories currently installed.) 83s Preparing to unpack .../0-libdeflate0_1.23-2_arm64.deb ... 83s Unpacking libdeflate0:arm64 (1.23-2) ... 83s Selecting previously unselected package libhtscodecs2:arm64. 83s Preparing to unpack .../1-libhtscodecs2_1.6.1-2_arm64.deb ... 83s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 83s Selecting previously unselected package libhts3t64:arm64. 83s Preparing to unpack .../2-libhts3t64_1.21+ds-1_arm64.deb ... 83s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 83s Selecting previously unselected package python3-pysam. 83s Preparing to unpack .../3-python3-pysam_0.23.0+ds-1build1_arm64.deb ... 83s Unpacking python3-pysam (0.23.0+ds-1build1) ... 83s Selecting previously unselected package atropos. 83s Preparing to unpack .../4-atropos_1.1.32+dfsg-2build2_arm64.deb ... 83s Unpacking atropos (1.1.32+dfsg-2build2) ... 83s Selecting previously unselected package python3-all. 83s Preparing to unpack .../5-python3-all_3.13.7-1_arm64.deb ... 83s Unpacking python3-all (3.13.7-1) ... 83s Selecting previously unselected package python3-iniconfig. 83s Preparing to unpack .../6-python3-iniconfig_1.1.1-2_all.deb ... 83s Unpacking python3-iniconfig (1.1.1-2) ... 83s Selecting previously unselected package python3-packaging. 83s Preparing to unpack .../7-python3-packaging_25.0-1_all.deb ... 83s Unpacking python3-packaging (25.0-1) ... 83s Selecting previously unselected package python3-pluggy. 83s Preparing to unpack .../8-python3-pluggy_1.6.0-1_all.deb ... 83s Unpacking python3-pluggy (1.6.0-1) ... 83s Selecting previously unselected package python3-pytest. 83s Preparing to unpack .../9-python3-pytest_8.4.2-1_all.deb ... 83s Unpacking python3-pytest (8.4.2-1) ... 83s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 83s Setting up python3-iniconfig (1.1.1-2) ... 84s Setting up libdeflate0:arm64 (1.23-2) ... 84s Setting up python3-all (3.13.7-1) ... 84s Setting up python3-packaging (25.0-1) ... 84s Setting up python3-pluggy (1.6.0-1) ... 84s Setting up libhts3t64:arm64 (1.21+ds-1) ... 84s Setting up python3-pysam (0.23.0+ds-1build1) ... 84s Setting up python3-pytest (8.4.2-1) ... 84s Setting up atropos (1.1.32+dfsg-2build2) ... 85s Processing triggers for man-db (2.13.1-1) ... 86s Processing triggers for libc-bin (2.42-0ubuntu3) ... 87s autopkgtest [19:47:43]: test run-unit-test: [----------------------- 88s ============================= test session starts ============================== 88s platform linux -- Python 3.13.7, pytest-8.4.2, pluggy-1.6.0 -- /usr/bin/python3.13 88s cachedir: .pytest_cache 88s rootdir: /tmp/autopkgtest.szCkVq/autopkgtest_tmp 88s plugins: typeguard-4.4.2 94s collecting ... collected 222 items 94s 94s tests/test_adapters.py::test_issue_52 PASSED [ 0%] 94s tests/test_adapters.py::test_issue_80 PASSED [ 0%] 94s tests/test_adapters.py::test_str PASSED [ 1%] 94s tests/test_adapters.py::test_color PASSED [ 1%] 94s tests/test_adapters.py::test_parse_braces PASSED [ 2%] 94s tests/test_adapters.py::test_parse_braces_fail PASSED [ 2%] 94s tests/test_adapters.py::test_linked_adapter PASSED [ 3%] 94s tests/test_adapters.py::test_random_match_probabilities PASSED [ 3%] 94s tests/test_align.py::TestAligner::test PASSED [ 4%] 94s tests/test_align.py::TestAligner::test_100_percent_error_rate PASSED [ 4%] 94s tests/test_align.py::test_polya PASSED [ 4%] 94s tests/test_align.py::test_compare_prefixes PASSED [ 5%] 94s tests/test_align.py::test_compare_suffixes PASSED [ 5%] 94s tests/test_align.py::test_wildcards_in_adapter PASSED [ 6%] 94s tests/test_align.py::test_wildcards_in_read PASSED [ 6%] 94s tests/test_align.py::test_wildcards_in_both PASSED [ 7%] 94s tests/test_align.py::test_no_match PASSED [ 7%] 94s tests/test_align.py::test_factorial PASSED [ 8%] 94s tests/test_align.py::test_match_probability PASSED [ 8%] 94s tests/test_align.py::test_insert_align PASSED [ 9%] 94s tests/test_align.py::test_short_adapter_overlap PASSED [ 9%] 94s tests/test_align.py::test_insert_align_different_lengths PASSED [ 9%] 94s tests/test_align.py::test_multi_aligner_no_mismatches PASSED [ 10%] 94s tests/test_align.py::test_multi_aligner_with_mismatches PASSED [ 10%] 95s tests/test_atropos.py::test_example PASSED [ 11%] 95s tests/test_atropos.py::test_small PASSED [ 11%] 95s tests/test_atropos.py::test_empty PASSED [ 12%] 95s tests/test_atropos.py::test_newlines PASSED [ 12%] 95s tests/test_atropos.py::test_lowercase PASSED [ 13%] 95s tests/test_atropos.py::test_rest PASSED [ 13%] 95s tests/test_atropos.py::test_restfront PASSED [ 13%] 95s tests/test_atropos.py::test_discard PASSED [ 14%] 95s tests/test_atropos.py::test_discard_untrimmed PASSED [ 14%] 95s tests/test_atropos.py::test_plus PASSED [ 15%] 95s tests/test_atropos.py::test_extensiontxtgz PASSED [ 15%] 95s tests/test_atropos.py::test_format PASSED [ 16%] 95s tests/test_atropos.py::test_minimum_length PASSED [ 16%] 95s tests/test_atropos.py::test_too_short PASSED [ 17%] 95s tests/test_atropos.py::test_too_short_no_primer PASSED [ 17%] 95s tests/test_atropos.py::test_maximum_length PASSED [ 18%] 95s tests/test_atropos.py::test_too_long PASSED [ 18%] 95s tests/test_atropos.py::test_length_tag PASSED [ 18%] 95s tests/test_atropos.py::test_overlap_a PASSED [ 19%] 95s tests/test_atropos.py::test_overlap_b PASSED [ 19%] 95s tests/test_atropos.py::test_qualtrim PASSED [ 20%] 95s tests/test_atropos.py::test_qualbase PASSED [ 20%] 95s tests/test_atropos.py::test_quality_trim_only PASSED [ 21%] 95s tests/test_atropos.py::test_twoadapters PASSED [ 21%] 95s tests/test_atropos.py::test_polya PASSED [ 22%] 95s tests/test_atropos.py::test_polya_brace_notation PASSED [ 22%] 95s tests/test_atropos.py::test_mask_adapter PASSED [ 22%] 95s tests/test_atropos.py::test_gz_multiblock PASSED [ 23%] 95s tests/test_atropos.py::test_suffix PASSED [ 23%] 95s tests/test_atropos.py::test_read_wildcard PASSED [ 24%] 95s tests/test_atropos.py::test_adapter_wildcard PASSED [ 24%] 95s tests/test_atropos.py::test_wildcard_N PASSED [ 25%] 95s tests/test_atropos.py::test_illumina_adapter_wildcard PASSED [ 25%] 95s tests/test_atropos.py::test_adapter_front PASSED [ 26%] 95s tests/test_atropos.py::test_literal_N PASSED [ 26%] 95s tests/test_atropos.py::test_literal_N2 PASSED [ 27%] 95s tests/test_atropos.py::test_literal_N_brace_notation PASSED [ 27%] 95s tests/test_atropos.py::test_literal_N2_brace_notation PASSED [ 27%] 95s tests/test_atropos.py::test_anchored_front PASSED [ 28%] 95s tests/test_atropos.py::test_anchored_front_ellipsis_notation PASSED [ 28%] 95s tests/test_atropos.py::test_anchored_back PASSED [ 29%] 95s tests/test_atropos.py::test_anchored_back_no_indels PASSED [ 29%] 95s tests/test_atropos.py::test_no_indels PASSED [ 30%] 95s tests/test_atropos.py::test_issue_46 PASSED [ 30%] 95s tests/test_atropos.py::test_strip_suffix PASSED [ 31%] 95s tests/test_atropos.py::test_info_file PASSED [ 31%] 95s tests/test_atropos.py::test_info_file_times PASSED [ 31%] 95s tests/test_atropos.py::test_info_file_fasta PASSED [ 32%] 95s tests/test_atropos.py::test_named_adapter PASSED [ 32%] 95s tests/test_atropos.py::test_adapter_with_U PASSED [ 33%] 95s tests/test_atropos.py::test_no_trim PASSED [ 33%] 95s tests/test_atropos.py::test_bzip2 PASSED [ 34%] 95s tests/test_atropos.py::test_xz PASSED [ 34%] 95s tests/test_atropos.py::test_qualfile_only PASSED [ 35%] 95s tests/test_atropos.py::test_no_args PASSED [ 35%] 95s tests/test_atropos.py::test_two_fastqs PASSED [ 36%] 95s tests/test_atropos.py::test_anchored_no_indels PASSED [ 36%] 95s tests/test_atropos.py::test_anchored_no_indels_wildcard_read PASSED [ 36%] 95s tests/test_atropos.py::test_anchored_no_indels_wildcard_adapt PASSED [ 37%] 95s tests/test_atropos.py::test_unconditional_cut_front PASSED [ 37%] 95s tests/test_atropos.py::test_unconditional_cut_back PASSED [ 38%] 95s tests/test_atropos.py::test_unconditional_cut_both PASSED [ 38%] 95s tests/test_atropos.py::test_untrimmed_output PASSED [ 39%] 95s tests/test_atropos.py::test_adapter_file PASSED [ 39%] 95s tests/test_atropos.py::test_adapter_file_5p_anchored PASSED [ 40%] 95s tests/test_atropos.py::test_adapter_file_3p_anchored PASSED [ 40%] 95s tests/test_atropos.py::test_adapter_file_5p_anchored_no_indels PASSED [ 40%] 95s tests/test_atropos.py::test_adapter_file_3p_anchored_no_indels PASSED [ 41%] 95s tests/test_atropos.py::test_demultiplex PASSED [ 41%] 95s tests/test_atropos.py::test_max_n PASSED [ 42%] 95s tests/test_atropos.py::test_quiet_is_quiet PASSED [ 42%] 95s tests/test_atropos.py::test_nextseq PASSED [ 43%] 95s tests/test_atropos.py::test_linked PASSED [ 43%] 95s tests/test_atropos.py::test_fasta PASSED [ 44%] 95s tests/test_atropos.py::test_custom_bisulfite_1 PASSED [ 44%] 95s tests/test_atropos.py::test_custom_bisulfite_2 PASSED [ 45%] 95s tests/test_atropos.py::test_custom_bisulfite_3 PASSED [ 45%] 95s tests/test_atropos.py::test_custom_bisulfite_4 PASSED [ 45%] 95s tests/test_atropos.py::test_sra SKIPPED (No internet connection or s...) [ 46%] 95s tests/test_colorspace.py::test_encode PASSED [ 46%] 95s tests/test_colorspace.py::test_decode PASSED [ 47%] 95s tests/test_colorspace.py::test_qualtrim_csfastaqual PASSED [ 47%] 95s tests/test_colorspace.py::test_E3M PASSED [ 48%] 95s tests/test_colorspace.py::test_bwa PASSED [ 48%] 95s tests/test_colorspace.py::test_bfast PASSED [ 49%] 96s tests/test_colorspace.py::test_trim_095 PASSED [ 49%] 96s tests/test_colorspace.py::test_solid PASSED [ 50%] 96s tests/test_colorspace.py::test_solid_basespace_adapter PASSED [ 50%] 96s tests/test_colorspace.py::test_solid5p PASSED [ 50%] 96s tests/test_colorspace.py::test_solid5p_prefix_notrim PASSED [ 51%] 96s tests/test_colorspace.py::test_solid5p_prefix PASSED [ 51%] 96s tests/test_colorspace.py::test_solid5p_fastq PASSED [ 52%] 96s tests/test_colorspace.py::test_solid5p_prefix_notrim_fastq PASSED [ 52%] 96s tests/test_colorspace.py::test_solid5p_prefix_fastq PASSED [ 53%] 96s tests/test_colorspace.py::test_sra_fastq PASSED [ 53%] 96s tests/test_colorspace.py::test_no_zero_cap PASSED [ 54%] 96s tests/test_commands.py::test_order_preserving_writer PASSED [ 54%] 96s tests/test_filters.py::test_ncontentfilter PASSED [ 54%] 96s tests/test_filters.py::test_ncontentfilter_paired PASSED [ 55%] 96s tests/test_modifiers.py::test_unconditional_cutter PASSED [ 55%] 96s tests/test_modifiers.py::test_nend_trimmer PASSED [ 56%] 96s tests/test_modifiers.py::test_quality_trimmer PASSED [ 56%] 96s tests/test_modifiers.py::test_Modifiers_single PASSED [ 57%] 96s tests/test_modifiers.py::test_Modifiers_paired_legacy PASSED [ 57%] 96s tests/test_modifiers.py::test_Modifiers_paired_both PASSED [ 58%] 96s tests/test_modifiers.py::test_min_cutter_T_T PASSED [ 58%] 96s tests/test_modifiers.py::test_min_cutter_F_T PASSED [ 59%] 96s tests/test_modifiers.py::test_min_cutter_T_F PASSED [ 59%] 96s tests/test_modifiers.py::test_non_directional_bisulfite_trimmer PASSED [ 59%] 96s tests/test_modifiers.py::test_TruSeq_trimmer PASSED [ 60%] 96s tests/test_modifiers.py::test_Swift_trimmer PASSED [ 60%] 96s tests/test_modifiers.py::test_overlapping PASSED [ 61%] 96s tests/test_modifiers.py::test_overlapping_with_error_correction PASSED [ 61%] 96s tests/test_modifiers.py::test_mismatched_adapter_overlaps PASSED [ 62%] 96s tests/test_modifiers.py::test_error_correction PASSED [ 62%] 96s tests/test_modifiers.py::test_error_correction_no_insert_match_one_adapter_match PASSED [ 63%] 96s tests/test_modifiers.py::test_error_correction_no_insert_match_two_adapter_matches PASSED [ 63%] 96s tests/test_modifiers.py::test_error_correction_unequal_read_lengths PASSED [ 63%] 96s tests/test_modifiers.py::test_overwrite_read PASSED [ 64%] 96s tests/test_multicore.py::test_wait_on PASSED [ 64%] 98s tests/test_multicore.py::test_timeout PASSED [ 65%] 98s tests/test_multicore.py::test_enqueue_dequeue PASSED [ 65%] 102s tests/test_multicore.py::test_enqueue_timeout PASSED [ 66%] 106s tests/test_multicore.py::test_dequeue_timeout PASSED [ 66%] 106s tests/test_paired.py::test_paired_separate PASSED [ 67%] 106s tests/test_paired.py::test_paired_end_legacy PASSED [ 67%] 106s tests/test_paired.py::test_untrimmed_paired_output PASSED [ 68%] 106s tests/test_paired.py::test_explicit_format_with_paired PASSED [ 68%] 106s tests/test_paired.py::test_no_trimming_legacy PASSED [ 68%] 106s tests/test_paired.py::test_no_trimming PASSED [ 69%] 106s tests/test_paired.py::test_missing_file PASSED [ 69%] 106s tests/test_paired.py::test_first_too_short PASSED [ 70%] 106s tests/test_paired.py::test_second_too_short PASSED [ 70%] 106s tests/test_paired.py::test_unmatched_read_names PASSED [ 71%] 106s tests/test_paired.py::test_legacy_minlength PASSED [ 71%] 106s tests/test_paired.py::test_paired_end PASSED [ 72%] 106s tests/test_paired.py::test_paired_anchored_back_no_indels PASSED [ 72%] 106s tests/test_paired.py::test_paired_end_qualtrim PASSED [ 72%] 106s tests/test_paired.py::test_paired_end_qualtrim_swapped PASSED [ 73%] 106s tests/test_paired.py::test_paired_end_cut PASSED [ 73%] 106s tests/test_paired.py::test_paired_end_A_only PASSED [ 74%] 106s tests/test_paired.py::test_paired_end_mask_adapter PASSED [ 74%] 106s tests/test_paired.py::test_discard_untrimmed PASSED [ 75%] 106s tests/test_paired.py::test_discard_trimmed PASSED [ 75%] 106s tests/test_paired.py::test_interleaved PASSED [ 76%] 106s tests/test_paired.py::test_interleaved_no_paired_output PASSED [ 76%] 106s tests/test_paired.py::test_pair_filter PASSED [ 77%] 106s tests/test_paired.py::test_too_short_paired_output PASSED [ 77%] 106s tests/test_paired.py::test_too_long_output PASSED [ 77%] 106s tests/test_paired.py::test_too_short_output_paired_option_missing PASSED [ 78%] 106s tests/test_paired.py::test_custom_bisulfite_1 PASSED [ 78%] 106s tests/test_paired.py::test_custom_bisulfite_2 PASSED [ 79%] 106s tests/test_paired.py::test_no_insert_match PASSED [ 79%] 106s tests/test_paired.py::test_overwrite PASSED [ 80%] 116s tests/test_paired.py::test_no_writer_process PASSED [ 80%] 127s tests/test_paired.py::test_summary PASSED [ 81%] 127s tests/test_qualtrim.py::test_nextseq_trim PASSED [ 81%] 127s tests/test_seqio.py::TestAlphabet::test_alphabet PASSED [ 81%] 127s tests/test_seqio.py::TestSequence::test_too_many_qualities PASSED [ 82%] 127s tests/test_seqio.py::TestSequence::test_too_many_qualities_colorspace PASSED [ 82%] 127s tests/test_seqio.py::TestSequence::test_invalid_primer PASSED [ 83%] 127s tests/test_seqio.py::TestFastaReader::test PASSED [ 83%] 127s tests/test_seqio.py::TestFastaReader::test_with_comments PASSED [ 84%] 127s tests/test_seqio.py::TestFastaReader::test_wrong_format PASSED [ 84%] 127s tests/test_seqio.py::TestFastaReader::test_fastareader_keeplinebreaks PASSED [ 85%] 127s tests/test_seqio.py::TestFastaReader::test_context_manager PASSED [ 85%] 127s tests/test_seqio.py::TestFastqReader::test_fastqreader PASSED [ 86%] 127s tests/test_seqio.py::TestFastqReader::test_fastqreader_dos PASSED [ 86%] 127s tests/test_seqio.py::TestFastqReader::test_fastq_wrongformat PASSED [ 86%] 127s tests/test_seqio.py::TestFastqReader::test_fastq_incomplete PASSED [ 87%] 127s tests/test_seqio.py::TestFastqReader::test_context_manager PASSED [ 87%] 127s tests/test_seqio.py::TestFastqReader::test_alphabet PASSED [ 88%] 127s tests/test_seqio.py::TestFastaQualReader::test_mismatching_read_names PASSED [ 88%] 127s tests/test_seqio.py::TestFastaQualReader::test_invalid_quality_value PASSED [ 89%] 127s tests/test_seqio.py::TestSeqioOpen::test_sequence_reader PASSED [ 89%] 127s tests/test_seqio.py::TestSeqioOpen::test_autodetect_fasta_format PASSED [ 90%] 127s tests/test_seqio.py::TestSeqioOpen::test_write_qualities_to_fasta PASSED [ 90%] 127s tests/test_seqio.py::TestSeqioOpen::test_autodetect_fastq_format PASSED [ 90%] 127s tests/test_seqio.py::TestSeqioOpen::test_fastq_qualities_missing PASSED [ 91%] 127s tests/test_seqio.py::TestInterleavedReader::test PASSED [ 91%] 127s tests/test_seqio.py::TestInterleavedReader::test_missing_partner PASSED [ 92%] 127s tests/test_seqio.py::TestInterleavedReader::test_incorrectly_paired PASSED [ 92%] 127s tests/test_seqio.py::TestFastaWriter::test PASSED [ 93%] 127s tests/test_seqio.py::TestFastaWriter::test_linelength PASSED [ 93%] 127s tests/test_seqio.py::TestFastaWriter::test_write_sequence_object PASSED [ 94%] 127s tests/test_seqio.py::TestFastaWriter::test_write_zero_length_sequence PASSED [ 94%] 127s tests/test_seqio.py::TestFastqWriter::test PASSED [ 95%] 127s tests/test_seqio.py::TestFastqWriter::test_twoheaders PASSED [ 95%] 127s tests/test_seqio.py::TestInterleavedWriter::test PASSED [ 95%] 127s tests/test_seqio.py::TestPairedSequenceReader::test_sequence_names_match PASSED [ 96%] 127s tests/test_seqio.py::test_truncated_gz PASSED [ 96%] 127s tests/test_seqio.py::test_truncated_gz_iter PASSED [ 97%] 127s tests/test_trim.py::test_cs_5p PASSED [ 97%] 127s tests/test_trim.py::test_statistics PASSED [ 98%] 127s tests/test_xopen.py::test_context_manager PASSED [ 98%] 127s tests/test_xopen.py::test_append PASSED [ 99%] 127s tests/test_xopen.py::test_xopen_text PASSED [ 99%] 127s tests/test_xopen.py::test_xopen_binary PASSED [100%] 127s 127s =============================== warnings summary =============================== 127s tests/test_paired.py:638 127s /tmp/autopkgtest.szCkVq/autopkgtest_tmp/tests/test_paired.py:638: PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 127s @pytest.mark.timeout(10) 127s 127s tests/test_paired.py::test_no_writer_process 127s tests/test_paired.py::test_no_writer_process 127s tests/test_paired.py::test_summary 127s tests/test_paired.py::test_summary 127s /usr/lib/python3.13/multiprocessing/popen_fork.py:67: DeprecationWarning: This process (pid=1910) is multi-threaded, use of fork() may lead to deadlocks in the child. 127s self.pid = os.fork() 127s 127s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 127s ================= 221 passed, 1 skipped, 5 warnings in 38.71s ================== 127s autopkgtest [19:48:23]: test run-unit-test: -----------------------] 128s run-unit-test PASS 128s autopkgtest [19:48:24]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 129s autopkgtest [19:48:25]: @@@@@@@@@@@@@@@@@@@@ summary 129s run-unit-test PASS