0s autopkgtest [21:12:38]: starting date and time: 2025-10-21 21:12:38+0000 0s autopkgtest [21:12:38]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [21:12:38]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.l2zqss2f/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-ppc64el-10.secgroup --name adt-resolute-ppc64el-atropos-20251021-211238-juju-7f2275-prod-proposed-migration-environment-2-f2c32055-8bf9-42b0-bd6b-136ba4be63c8 --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-ppc64el-atropos-20251021-211238-juju-7f2275-prod-proposed-migration-environment-2-f2c32055-8bf9-42b0-bd6b-136ba4be63c8 from image adt/ubuntu-resolute-ppc64el-server-20251021.img (UUID c177abc7-cbc1-4b1f-967f-196ea722a402)... 53s autopkgtest [21:13:31]: testbed dpkg architecture: ppc64el 53s autopkgtest [21:13:31]: testbed apt version: 3.1.8ubuntu1 53s autopkgtest [21:13:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 54s autopkgtest [21:13:32]: testbed release detected to be: None 54s autopkgtest [21:13:32]: updating testbed package index (apt update) 55s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 55s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 55s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 55s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 55s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.0 kB] 55s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [627 kB] 55s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [62.2 kB] 55s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 55s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [119 kB] 55s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted ppc64el Packages [940 B] 55s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [427 kB] 56s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [4596 B] 56s Fetched 1344 kB in 1s (1323 kB/s) 56s Reading package lists... 57s Failed to check for VM: Permission denied 57s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 57s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 57s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 57s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 58s Reading package lists... 58s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Calculating upgrade... 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 59s autopkgtest [21:13:37]: upgrading testbed (apt dist-upgrade and autopurge) 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Calculating upgrade... 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 59s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Solving dependencies... 60s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 62s autopkgtest [21:13:40]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:02:41 UTC 2025 63s autopkgtest [21:13:41]: @@@@@@@@@@@@@@@@@@@@ apt-source atropos 65s Get:1 http://ftpmaster.internal/ubuntu resolute/universe atropos 1.1.32+dfsg-2build2 (dsc) [2258 B] 65s Get:2 http://ftpmaster.internal/ubuntu resolute/universe atropos 1.1.32+dfsg-2build2 (tar) [3117 kB] 65s Get:3 http://ftpmaster.internal/ubuntu resolute/universe atropos 1.1.32+dfsg-2build2 (diff) [6900 B] 65s gpgv: Signature made Tue Mar 4 15:39:30 2025 UTC 65s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 65s gpgv: Can't check signature: No public key 65s dpkg-source: warning: cannot verify inline signature for ./atropos_1.1.32+dfsg-2build2.dsc: no acceptable signature found 65s autopkgtest [21:13:43]: testing package atropos version 1.1.32+dfsg-2build2 66s autopkgtest [21:13:44]: build not needed 66s autopkgtest [21:13:44]: test run-unit-test: preparing testbed 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Solving dependencies... 67s The following NEW packages will be installed: 67s atropos libdeflate0 libhts3t64 libhtscodecs2 python3-all python3-iniconfig 67s python3-packaging python3-pluggy python3-pysam python3-pytest 67s 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 67s Need to get 5395 kB of archives. 67s After this operation, 43.1 MB of additional disk space will be used. 67s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2 [63.3 kB] 67s Get:2 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhtscodecs2 ppc64el 1.6.1-2 [113 kB] 67s Get:3 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhts3t64 ppc64el 1.21+ds-1 [585 kB] 68s Get:4 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pysam ppc64el 0.23.0+ds-1build1 [4039 kB] 68s Get:5 http://ftpmaster.internal/ubuntu resolute/universe ppc64el atropos ppc64el 1.1.32+dfsg-2build2 [245 kB] 68s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-all ppc64el 3.13.7-1 [884 B] 68s Get:7 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 68s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-packaging all 25.0-1 [52.8 kB] 68s Get:9 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pluggy all 1.6.0-1 [21.0 kB] 68s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el python3-pytest all 8.4.2-1 [268 kB] 68s Fetched 5395 kB in 1s (5366 kB/s) 68s Selecting previously unselected package libdeflate0:ppc64el. 68s (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 ... 76480 files and directories currently installed.) 68s Preparing to unpack .../0-libdeflate0_1.23-2_ppc64el.deb ... 68s Unpacking libdeflate0:ppc64el (1.23-2) ... 68s Selecting previously unselected package libhtscodecs2:ppc64el. 68s Preparing to unpack .../1-libhtscodecs2_1.6.1-2_ppc64el.deb ... 68s Unpacking libhtscodecs2:ppc64el (1.6.1-2) ... 68s Selecting previously unselected package libhts3t64:ppc64el. 68s Preparing to unpack .../2-libhts3t64_1.21+ds-1_ppc64el.deb ... 68s Unpacking libhts3t64:ppc64el (1.21+ds-1) ... 68s Selecting previously unselected package python3-pysam. 68s Preparing to unpack .../3-python3-pysam_0.23.0+ds-1build1_ppc64el.deb ... 68s Unpacking python3-pysam (0.23.0+ds-1build1) ... 69s Selecting previously unselected package atropos. 69s Preparing to unpack .../4-atropos_1.1.32+dfsg-2build2_ppc64el.deb ... 69s Unpacking atropos (1.1.32+dfsg-2build2) ... 69s Selecting previously unselected package python3-all. 69s Preparing to unpack .../5-python3-all_3.13.7-1_ppc64el.deb ... 69s Unpacking python3-all (3.13.7-1) ... 69s Selecting previously unselected package python3-iniconfig. 69s Preparing to unpack .../6-python3-iniconfig_1.1.1-2_all.deb ... 69s Unpacking python3-iniconfig (1.1.1-2) ... 69s Selecting previously unselected package python3-packaging. 69s Preparing to unpack .../7-python3-packaging_25.0-1_all.deb ... 69s Unpacking python3-packaging (25.0-1) ... 69s Selecting previously unselected package python3-pluggy. 69s Preparing to unpack .../8-python3-pluggy_1.6.0-1_all.deb ... 69s Unpacking python3-pluggy (1.6.0-1) ... 69s Selecting previously unselected package python3-pytest. 69s Preparing to unpack .../9-python3-pytest_8.4.2-1_all.deb ... 69s Unpacking python3-pytest (8.4.2-1) ... 69s Setting up libhtscodecs2:ppc64el (1.6.1-2) ... 69s Setting up python3-iniconfig (1.1.1-2) ... 69s Setting up libdeflate0:ppc64el (1.23-2) ... 69s Setting up python3-all (3.13.7-1) ... 69s Setting up python3-packaging (25.0-1) ... 69s Setting up python3-pluggy (1.6.0-1) ... 69s Setting up libhts3t64:ppc64el (1.21+ds-1) ... 69s Setting up python3-pysam (0.23.0+ds-1build1) ... 69s Setting up python3-pytest (8.4.2-1) ... 70s Setting up atropos (1.1.32+dfsg-2build2) ... 70s Processing triggers for man-db (2.13.1-1) ... 71s Processing triggers for libc-bin (2.42-0ubuntu3) ... 71s autopkgtest [21:13:49]: test run-unit-test: [----------------------- 72s ============================= test session starts ============================== 72s platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0 -- /usr/bin/python3.13 72s cachedir: .pytest_cache 72s rootdir: /tmp/autopkgtest.kz8GfB/autopkgtest_tmp 72s plugins: typeguard-4.4.2 78s collecting ... collected 222 items 78s 78s tests/test_adapters.py::test_issue_52 PASSED [ 0%] 78s tests/test_adapters.py::test_issue_80 PASSED [ 0%] 78s tests/test_adapters.py::test_str PASSED [ 1%] 78s tests/test_adapters.py::test_color PASSED [ 1%] 78s tests/test_adapters.py::test_parse_braces PASSED [ 2%] 78s tests/test_adapters.py::test_parse_braces_fail PASSED [ 2%] 78s tests/test_adapters.py::test_linked_adapter PASSED [ 3%] 78s tests/test_adapters.py::test_random_match_probabilities PASSED [ 3%] 78s tests/test_align.py::TestAligner::test PASSED [ 4%] 78s tests/test_align.py::TestAligner::test_100_percent_error_rate PASSED [ 4%] 78s tests/test_align.py::test_polya PASSED [ 4%] 78s tests/test_align.py::test_compare_prefixes PASSED [ 5%] 78s tests/test_align.py::test_compare_suffixes PASSED [ 5%] 78s tests/test_align.py::test_wildcards_in_adapter PASSED [ 6%] 78s tests/test_align.py::test_wildcards_in_read PASSED [ 6%] 78s tests/test_align.py::test_wildcards_in_both PASSED [ 7%] 78s tests/test_align.py::test_no_match PASSED [ 7%] 78s tests/test_align.py::test_factorial PASSED [ 8%] 78s tests/test_align.py::test_match_probability PASSED [ 8%] 78s tests/test_align.py::test_insert_align PASSED [ 9%] 78s tests/test_align.py::test_short_adapter_overlap PASSED [ 9%] 78s tests/test_align.py::test_insert_align_different_lengths PASSED [ 9%] 78s tests/test_align.py::test_multi_aligner_no_mismatches PASSED [ 10%] 78s tests/test_align.py::test_multi_aligner_with_mismatches PASSED [ 10%] 79s tests/test_atropos.py::test_example PASSED [ 11%] 79s tests/test_atropos.py::test_small PASSED [ 11%] 79s tests/test_atropos.py::test_empty PASSED [ 12%] 79s tests/test_atropos.py::test_newlines PASSED [ 12%] 79s tests/test_atropos.py::test_lowercase PASSED [ 13%] 79s tests/test_atropos.py::test_rest PASSED [ 13%] 79s tests/test_atropos.py::test_restfront PASSED [ 13%] 79s tests/test_atropos.py::test_discard PASSED [ 14%] 79s tests/test_atropos.py::test_discard_untrimmed PASSED [ 14%] 79s tests/test_atropos.py::test_plus PASSED [ 15%] 79s tests/test_atropos.py::test_extensiontxtgz PASSED [ 15%] 79s tests/test_atropos.py::test_format PASSED [ 16%] 79s tests/test_atropos.py::test_minimum_length PASSED [ 16%] 79s tests/test_atropos.py::test_too_short PASSED [ 17%] 79s tests/test_atropos.py::test_too_short_no_primer PASSED [ 17%] 79s tests/test_atropos.py::test_maximum_length PASSED [ 18%] 79s tests/test_atropos.py::test_too_long PASSED [ 18%] 79s tests/test_atropos.py::test_length_tag PASSED [ 18%] 79s tests/test_atropos.py::test_overlap_a PASSED [ 19%] 79s tests/test_atropos.py::test_overlap_b PASSED [ 19%] 79s tests/test_atropos.py::test_qualtrim PASSED [ 20%] 79s tests/test_atropos.py::test_qualbase PASSED [ 20%] 79s tests/test_atropos.py::test_quality_trim_only PASSED [ 21%] 79s tests/test_atropos.py::test_twoadapters PASSED [ 21%] 79s tests/test_atropos.py::test_polya PASSED [ 22%] 79s tests/test_atropos.py::test_polya_brace_notation PASSED [ 22%] 79s tests/test_atropos.py::test_mask_adapter PASSED [ 22%] 79s tests/test_atropos.py::test_gz_multiblock PASSED [ 23%] 79s tests/test_atropos.py::test_suffix PASSED [ 23%] 79s tests/test_atropos.py::test_read_wildcard PASSED [ 24%] 79s tests/test_atropos.py::test_adapter_wildcard PASSED [ 24%] 79s tests/test_atropos.py::test_wildcard_N PASSED [ 25%] 79s tests/test_atropos.py::test_illumina_adapter_wildcard PASSED [ 25%] 79s tests/test_atropos.py::test_adapter_front PASSED [ 26%] 79s tests/test_atropos.py::test_literal_N PASSED [ 26%] 79s tests/test_atropos.py::test_literal_N2 PASSED [ 27%] 79s tests/test_atropos.py::test_literal_N_brace_notation PASSED [ 27%] 79s tests/test_atropos.py::test_literal_N2_brace_notation PASSED [ 27%] 79s tests/test_atropos.py::test_anchored_front PASSED [ 28%] 79s tests/test_atropos.py::test_anchored_front_ellipsis_notation PASSED [ 28%] 79s tests/test_atropos.py::test_anchored_back PASSED [ 29%] 79s tests/test_atropos.py::test_anchored_back_no_indels PASSED [ 29%] 79s tests/test_atropos.py::test_no_indels PASSED [ 30%] 79s tests/test_atropos.py::test_issue_46 PASSED [ 30%] 79s tests/test_atropos.py::test_strip_suffix PASSED [ 31%] 79s tests/test_atropos.py::test_info_file PASSED [ 31%] 79s tests/test_atropos.py::test_info_file_times PASSED [ 31%] 79s tests/test_atropos.py::test_info_file_fasta PASSED [ 32%] 79s tests/test_atropos.py::test_named_adapter PASSED [ 32%] 79s tests/test_atropos.py::test_adapter_with_U PASSED [ 33%] 79s tests/test_atropos.py::test_no_trim PASSED [ 33%] 79s tests/test_atropos.py::test_bzip2 PASSED [ 34%] 79s tests/test_atropos.py::test_xz PASSED [ 34%] 79s tests/test_atropos.py::test_qualfile_only PASSED [ 35%] 79s tests/test_atropos.py::test_no_args PASSED [ 35%] 79s tests/test_atropos.py::test_two_fastqs PASSED [ 36%] 79s tests/test_atropos.py::test_anchored_no_indels PASSED [ 36%] 79s tests/test_atropos.py::test_anchored_no_indels_wildcard_read PASSED [ 36%] 79s tests/test_atropos.py::test_anchored_no_indels_wildcard_adapt PASSED [ 37%] 79s tests/test_atropos.py::test_unconditional_cut_front PASSED [ 37%] 79s tests/test_atropos.py::test_unconditional_cut_back PASSED [ 38%] 79s tests/test_atropos.py::test_unconditional_cut_both PASSED [ 38%] 79s tests/test_atropos.py::test_untrimmed_output PASSED [ 39%] 79s tests/test_atropos.py::test_adapter_file PASSED [ 39%] 79s tests/test_atropos.py::test_adapter_file_5p_anchored PASSED [ 40%] 79s tests/test_atropos.py::test_adapter_file_3p_anchored PASSED [ 40%] 79s tests/test_atropos.py::test_adapter_file_5p_anchored_no_indels PASSED [ 40%] 79s tests/test_atropos.py::test_adapter_file_3p_anchored_no_indels PASSED [ 41%] 79s tests/test_atropos.py::test_demultiplex PASSED [ 41%] 79s tests/test_atropos.py::test_max_n PASSED [ 42%] 79s tests/test_atropos.py::test_quiet_is_quiet PASSED [ 42%] 79s tests/test_atropos.py::test_nextseq PASSED [ 43%] 79s tests/test_atropos.py::test_linked PASSED [ 43%] 79s tests/test_atropos.py::test_fasta PASSED [ 44%] 79s tests/test_atropos.py::test_custom_bisulfite_1 PASSED [ 44%] 79s tests/test_atropos.py::test_custom_bisulfite_2 PASSED [ 45%] 79s tests/test_atropos.py::test_custom_bisulfite_3 PASSED [ 45%] 79s tests/test_atropos.py::test_custom_bisulfite_4 PASSED [ 45%] 79s tests/test_atropos.py::test_sra SKIPPED (No internet connection or s...) [ 46%] 79s tests/test_colorspace.py::test_encode PASSED [ 46%] 79s tests/test_colorspace.py::test_decode PASSED [ 47%] 79s tests/test_colorspace.py::test_qualtrim_csfastaqual PASSED [ 47%] 79s tests/test_colorspace.py::test_E3M PASSED [ 48%] 79s tests/test_colorspace.py::test_bwa PASSED [ 48%] 79s tests/test_colorspace.py::test_bfast PASSED [ 49%] 79s tests/test_colorspace.py::test_trim_095 PASSED [ 49%] 79s tests/test_colorspace.py::test_solid PASSED [ 50%] 79s tests/test_colorspace.py::test_solid_basespace_adapter PASSED [ 50%] 79s tests/test_colorspace.py::test_solid5p PASSED [ 50%] 79s tests/test_colorspace.py::test_solid5p_prefix_notrim PASSED [ 51%] 79s tests/test_colorspace.py::test_solid5p_prefix PASSED [ 51%] 79s tests/test_colorspace.py::test_solid5p_fastq PASSED [ 52%] 79s tests/test_colorspace.py::test_solid5p_prefix_notrim_fastq PASSED [ 52%] 79s tests/test_colorspace.py::test_solid5p_prefix_fastq PASSED [ 53%] 79s tests/test_colorspace.py::test_sra_fastq PASSED [ 53%] 79s tests/test_colorspace.py::test_no_zero_cap PASSED [ 54%] 79s tests/test_commands.py::test_order_preserving_writer PASSED [ 54%] 79s tests/test_filters.py::test_ncontentfilter PASSED [ 54%] 79s tests/test_filters.py::test_ncontentfilter_paired PASSED [ 55%] 79s tests/test_modifiers.py::test_unconditional_cutter PASSED [ 55%] 79s tests/test_modifiers.py::test_nend_trimmer PASSED [ 56%] 79s tests/test_modifiers.py::test_quality_trimmer PASSED [ 56%] 79s tests/test_modifiers.py::test_Modifiers_single PASSED [ 57%] 79s tests/test_modifiers.py::test_Modifiers_paired_legacy PASSED [ 57%] 79s tests/test_modifiers.py::test_Modifiers_paired_both PASSED [ 58%] 79s tests/test_modifiers.py::test_min_cutter_T_T PASSED [ 58%] 79s tests/test_modifiers.py::test_min_cutter_F_T PASSED [ 59%] 79s tests/test_modifiers.py::test_min_cutter_T_F PASSED [ 59%] 79s tests/test_modifiers.py::test_non_directional_bisulfite_trimmer PASSED [ 59%] 79s tests/test_modifiers.py::test_TruSeq_trimmer PASSED [ 60%] 79s tests/test_modifiers.py::test_Swift_trimmer PASSED [ 60%] 79s tests/test_modifiers.py::test_overlapping PASSED [ 61%] 79s tests/test_modifiers.py::test_overlapping_with_error_correction PASSED [ 61%] 79s tests/test_modifiers.py::test_mismatched_adapter_overlaps PASSED [ 62%] 79s tests/test_modifiers.py::test_error_correction PASSED [ 62%] 79s tests/test_modifiers.py::test_error_correction_no_insert_match_one_adapter_match PASSED [ 63%] 79s tests/test_modifiers.py::test_error_correction_no_insert_match_two_adapter_matches PASSED [ 63%] 79s tests/test_modifiers.py::test_error_correction_unequal_read_lengths PASSED [ 63%] 79s tests/test_modifiers.py::test_overwrite_read PASSED [ 64%] 79s tests/test_multicore.py::test_wait_on PASSED [ 64%] 81s tests/test_multicore.py::test_timeout PASSED [ 65%] 81s tests/test_multicore.py::test_enqueue_dequeue PASSED [ 65%] 85s tests/test_multicore.py::test_enqueue_timeout PASSED [ 66%] 89s tests/test_multicore.py::test_dequeue_timeout PASSED [ 66%] 89s tests/test_paired.py::test_paired_separate PASSED [ 67%] 89s tests/test_paired.py::test_paired_end_legacy PASSED [ 67%] 89s tests/test_paired.py::test_untrimmed_paired_output PASSED [ 68%] 90s tests/test_paired.py::test_explicit_format_with_paired PASSED [ 68%] 90s tests/test_paired.py::test_no_trimming_legacy PASSED [ 68%] 90s tests/test_paired.py::test_no_trimming PASSED [ 69%] 90s tests/test_paired.py::test_missing_file PASSED [ 69%] 90s tests/test_paired.py::test_first_too_short PASSED [ 70%] 90s tests/test_paired.py::test_second_too_short PASSED [ 70%] 90s tests/test_paired.py::test_unmatched_read_names PASSED [ 71%] 90s tests/test_paired.py::test_legacy_minlength PASSED [ 71%] 90s tests/test_paired.py::test_paired_end PASSED [ 72%] 90s tests/test_paired.py::test_paired_anchored_back_no_indels PASSED [ 72%] 90s tests/test_paired.py::test_paired_end_qualtrim PASSED [ 72%] 90s tests/test_paired.py::test_paired_end_qualtrim_swapped PASSED [ 73%] 90s tests/test_paired.py::test_paired_end_cut PASSED [ 73%] 90s tests/test_paired.py::test_paired_end_A_only PASSED [ 74%] 90s tests/test_paired.py::test_paired_end_mask_adapter PASSED [ 74%] 90s tests/test_paired.py::test_discard_untrimmed PASSED [ 75%] 90s tests/test_paired.py::test_discard_trimmed PASSED [ 75%] 90s tests/test_paired.py::test_interleaved PASSED [ 76%] 90s tests/test_paired.py::test_interleaved_no_paired_output PASSED [ 76%] 90s tests/test_paired.py::test_pair_filter PASSED [ 77%] 90s tests/test_paired.py::test_too_short_paired_output PASSED [ 77%] 90s tests/test_paired.py::test_too_long_output PASSED [ 77%] 90s tests/test_paired.py::test_too_short_output_paired_option_missing PASSED [ 78%] 90s tests/test_paired.py::test_custom_bisulfite_1 PASSED [ 78%] 90s tests/test_paired.py::test_custom_bisulfite_2 PASSED [ 79%] 90s tests/test_paired.py::test_no_insert_match PASSED [ 79%] 90s tests/test_paired.py::test_overwrite PASSED [ 80%] 100s tests/test_paired.py::test_no_writer_process PASSED [ 80%] 110s tests/test_paired.py::test_summary PASSED [ 81%] 110s tests/test_qualtrim.py::test_nextseq_trim PASSED [ 81%] 110s tests/test_seqio.py::TestAlphabet::test_alphabet PASSED [ 81%] 110s tests/test_seqio.py::TestSequence::test_too_many_qualities PASSED [ 82%] 110s tests/test_seqio.py::TestSequence::test_too_many_qualities_colorspace PASSED [ 82%] 110s tests/test_seqio.py::TestSequence::test_invalid_primer PASSED [ 83%] 110s tests/test_seqio.py::TestFastaReader::test PASSED [ 83%] 110s tests/test_seqio.py::TestFastaReader::test_with_comments PASSED [ 84%] 110s tests/test_seqio.py::TestFastaReader::test_wrong_format PASSED [ 84%] 110s tests/test_seqio.py::TestFastaReader::test_fastareader_keeplinebreaks PASSED [ 85%] 110s tests/test_seqio.py::TestFastaReader::test_context_manager PASSED [ 85%] 110s tests/test_seqio.py::TestFastqReader::test_fastqreader PASSED [ 86%] 110s tests/test_seqio.py::TestFastqReader::test_fastqreader_dos PASSED [ 86%] 110s tests/test_seqio.py::TestFastqReader::test_fastq_wrongformat PASSED [ 86%] 110s tests/test_seqio.py::TestFastqReader::test_fastq_incomplete PASSED [ 87%] 110s tests/test_seqio.py::TestFastqReader::test_context_manager PASSED [ 87%] 110s tests/test_seqio.py::TestFastqReader::test_alphabet PASSED [ 88%] 110s tests/test_seqio.py::TestFastaQualReader::test_mismatching_read_names PASSED [ 88%] 110s tests/test_seqio.py::TestFastaQualReader::test_invalid_quality_value PASSED [ 89%] 110s tests/test_seqio.py::TestSeqioOpen::test_sequence_reader PASSED [ 89%] 110s tests/test_seqio.py::TestSeqioOpen::test_autodetect_fasta_format PASSED [ 90%] 110s tests/test_seqio.py::TestSeqioOpen::test_write_qualities_to_fasta PASSED [ 90%] 110s tests/test_seqio.py::TestSeqioOpen::test_autodetect_fastq_format PASSED [ 90%] 110s tests/test_seqio.py::TestSeqioOpen::test_fastq_qualities_missing PASSED [ 91%] 110s tests/test_seqio.py::TestInterleavedReader::test PASSED [ 91%] 110s tests/test_seqio.py::TestInterleavedReader::test_missing_partner PASSED [ 92%] 110s tests/test_seqio.py::TestInterleavedReader::test_incorrectly_paired PASSED [ 92%] 110s tests/test_seqio.py::TestFastaWriter::test PASSED [ 93%] 110s tests/test_seqio.py::TestFastaWriter::test_linelength PASSED [ 93%] 110s tests/test_seqio.py::TestFastaWriter::test_write_sequence_object PASSED [ 94%] 110s tests/test_seqio.py::TestFastaWriter::test_write_zero_length_sequence PASSED [ 94%] 110s tests/test_seqio.py::TestFastqWriter::test PASSED [ 95%] 110s tests/test_seqio.py::TestFastqWriter::test_twoheaders PASSED [ 95%] 110s tests/test_seqio.py::TestInterleavedWriter::test PASSED [ 95%] 110s tests/test_seqio.py::TestPairedSequenceReader::test_sequence_names_match PASSED [ 96%] 110s tests/test_seqio.py::test_truncated_gz PASSED [ 96%] 110s tests/test_seqio.py::test_truncated_gz_iter PASSED [ 97%] 110s tests/test_trim.py::test_cs_5p PASSED [ 97%] 110s tests/test_trim.py::test_statistics PASSED [ 98%] 110s tests/test_xopen.py::test_context_manager PASSED [ 98%] 110s tests/test_xopen.py::test_append PASSED [ 99%] 110s tests/test_xopen.py::test_xopen_text PASSED [ 99%] 110s tests/test_xopen.py::test_xopen_binary PASSED [100%] 110s 110s =============================== warnings summary =============================== 110s tests/test_paired.py:638 110s /tmp/autopkgtest.kz8GfB/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 110s @pytest.mark.timeout(10) 110s 110s tests/test_paired.py::test_no_writer_process 110s tests/test_paired.py::test_no_writer_process 110s tests/test_paired.py::test_summary 110s tests/test_paired.py::test_summary 110s /usr/lib/python3.13/multiprocessing/popen_fork.py:67: DeprecationWarning: This process (pid=1946) is multi-threaded, use of fork() may lead to deadlocks in the child. 110s self.pid = os.fork() 110s 110s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 110s ================= 221 passed, 1 skipped, 5 warnings in 38.12s ================== 111s autopkgtest [21:14:29]: test run-unit-test: -----------------------] 111s run-unit-test PASS 111s autopkgtest [21:14:29]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 111s autopkgtest [21:14:29]: @@@@@@@@@@@@@@@@@@@@ summary 111s run-unit-test PASS