0s autopkgtest [17:30:11]: starting date and time: 2026-02-05 17:30:11+0000 0s autopkgtest [17:30:11]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [17:30:11]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ij9si8dh/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:tqdm --apt-upgrade pycoqc --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=tqdm/4.67.3-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-arm64-37.secgroup --name adt-resolute-arm64-pycoqc-20260205-173009-juju-7f2275-prod-proposed-migration-environment-2-e5941958-8421-49a6-a1bb-ddd316fc0128 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 10s Creating nova instance adt-resolute-arm64-pycoqc-20260205-173009-juju-7f2275-prod-proposed-migration-environment-2-e5941958-8421-49a6-a1bb-ddd316fc0128 from image adt/ubuntu-resolute-arm64-server-20260205.img (UUID 88169191-3954-4b52-b471-25031b32a3a0)... 64s autopkgtest [17:31:15]: testbed dpkg architecture: arm64 64s autopkgtest [17:31:15]: testbed apt version: 3.1.14 65s autopkgtest [17:31:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 65s autopkgtest [17:31:16]: testbed release detected to be: None 66s autopkgtest [17:31:17]: updating testbed package index (apt update) 66s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 66s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 66s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 66s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 66s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1686 kB] 66s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [36.0 kB] 66s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [230 kB] 66s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 66s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [272 kB] 66s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [7520 B] 66s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [52.9 kB] 66s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [328 B] 66s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1512 kB] 66s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [42.6 kB] 67s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [27.1 kB] 67s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [800 B] 70s Fetched 3997 kB in 1s (4707 kB/s) 71s Reading package lists... 72s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 72s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 72s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 72s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 73s Reading package lists... 73s Reading package lists... 73s Building dependency tree... 73s Reading state information... 74s Calculating upgrade... 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s autopkgtest [17:31:25]: upgrading testbed (apt dist-upgrade and autopurge) 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 75s Calculating upgrade... 75s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s Reading package lists... 76s Building dependency tree... 76s Reading state information... 76s Solving dependencies... 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s autopkgtest [17:31:31]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:41:39 UTC 2026 80s autopkgtest [17:31:31]: @@@@@@@@@@@@@@@@@@@@ apt-source pycoqc 84s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (dsc) [2027 B] 84s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (tar) [41.6 MB] 84s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (diff) [6840 B] 84s gpgv: Signature made Sat Jan 18 02:09:23 2025 UTC 84s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 84s gpgv: issuer "tchet@debian.org" 84s gpgv: Can't check signature: No public key 84s dpkg-source: warning: cannot verify inline signature for ./pycoqc_2.5.2+dfsg-4.dsc: no acceptable signature found 86s autopkgtest [17:31:37]: testing package pycoqc version 2.5.2+dfsg-4 86s autopkgtest [17:31:37]: build not needed 91s autopkgtest [17:31:42]: test run-unit-test: preparing testbed 91s Reading package lists... 91s Building dependency tree... 91s Reading state information... 91s Solving dependencies... 92s The following NEW packages will be installed: 92s libblas3 libdeflate0 libgfortran5 libhdf5-310 libhdf5-hl-310 libhts3t64 92s libhtscodecs2 liblapack3 liblzf1 libqhull-r8.0 libsz2 pycoqc 92s python3-decorator python3-fastjsonschema python3-h5py python3-h5py-serial 92s python3-jupyter-core python3-nbformat python3-numpy python3-numpy-dev 92s python3-pandas python3-pandas-lib python3-platformdirs python3-plotly 92s python3-pysam python3-pytz python3-scipy python3-tenacity python3-tqdm 92s python3-traitlets 93s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 93s Need to get 45.7 MB of archives. 93s After this operation, 314 MB of additional disk space will be used. 93s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.3.5+ds-3 [366 kB] 93s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 93s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 93s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 93s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.3.5+ds-3 [4569 kB] 94s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 94s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 libsz2 arm64 1.1.5-1 [17.0 kB] 94s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-310 arm64 1.14.6+repack-2 [1287 kB] 94s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-hl-310 arm64 1.14.6+repack-2 [59.1 kB] 94s Get:10 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2build1 [83.8 kB] 94s Get:11 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhts3t64 arm64 1.22.1+ds2-1 [442 kB] 94s Get:12 http://ftpmaster.internal/ubuntu resolute/universe arm64 liblzf1 arm64 3.6-4build1 [7330 B] 94s Get:13 http://ftpmaster.internal/ubuntu resolute/universe arm64 libqhull-r8.0 arm64 2020.2-8 [191 kB] 94s Get:14 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-h5py-serial arm64 3.15.1-4 [1483 kB] 94s Get:15 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-h5py all 3.15.1-4 [11.3 kB] 94s Get:16 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytz all 2025.2-5 [32.4 kB] 94s Get:17 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.3.3+dfsg-3 [6290 kB] 95s Get:18 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.3.3+dfsg-3 [2948 kB] 96s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-decorator all 5.2.1-2 [28.1 kB] 96s Get:20 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fastjsonschema all 2.21.1-1 [20.4 kB] 96s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-platformdirs all 4.5.1-1 [17.1 kB] 96s Get:22 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-traitlets all 5.14.3+really5.14.3-2 [71.7 kB] 96s Get:23 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-jupyter-core all 5.9.1-1 [28.9 kB] 96s Get:24 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-nbformat all 5.10.4-1 [39.2 kB] 96s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-tenacity all 9.0.0-0ubuntu1 [17.0 kB] 96s Get:26 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-plotly all 5.20.0+dfsg-1.1 [2766 kB] 96s Get:27 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pysam arm64 0.23.3+ds-2 [4348 kB] 97s Get:28 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-scipy arm64 1.16.3-4 [17.5 MB] 99s Get:29 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-tqdm all 4.67.3-1 [93.3 kB] 100s Get:30 http://ftpmaster.internal/ubuntu resolute/universe arm64 pycoqc all 2.5.2+dfsg-4 [36.4 kB] 100s Fetched 45.7 MB in 8s (6000 kB/s) 100s Selecting previously unselected package python3-numpy-dev:arm64. 100s (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 ... 89360 files and directories currently installed.) 100s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_arm64.deb ... 100s Unpacking python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 100s Selecting previously unselected package libblas3:arm64. 100s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_arm64.deb ... 100s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 100s Selecting previously unselected package libgfortran5:arm64. 100s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_arm64.deb ... 100s Unpacking libgfortran5:arm64 (15.2.0-12ubuntu1) ... 100s Selecting previously unselected package liblapack3:arm64. 100s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 100s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 100s Selecting previously unselected package python3-numpy. 100s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_arm64.deb ... 100s Unpacking python3-numpy (1:2.3.5+ds-3) ... 101s Selecting previously unselected package libdeflate0:arm64. 101s Preparing to unpack .../05-libdeflate0_1.23-2_arm64.deb ... 101s Unpacking libdeflate0:arm64 (1.23-2) ... 101s Selecting previously unselected package libsz2:arm64. 101s Preparing to unpack .../06-libsz2_1.1.5-1_arm64.deb ... 101s Unpacking libsz2:arm64 (1.1.5-1) ... 101s Selecting previously unselected package libhdf5-310:arm64. 101s Preparing to unpack .../07-libhdf5-310_1.14.6+repack-2_arm64.deb ... 101s Unpacking libhdf5-310:arm64 (1.14.6+repack-2) ... 101s Selecting previously unselected package libhdf5-hl-310:arm64. 101s Preparing to unpack .../08-libhdf5-hl-310_1.14.6+repack-2_arm64.deb ... 101s Unpacking libhdf5-hl-310:arm64 (1.14.6+repack-2) ... 101s Selecting previously unselected package libhtscodecs2:arm64. 101s Preparing to unpack .../09-libhtscodecs2_1.6.1-2build1_arm64.deb ... 101s Unpacking libhtscodecs2:arm64 (1.6.1-2build1) ... 101s Selecting previously unselected package libhts3t64:arm64. 101s Preparing to unpack .../10-libhts3t64_1.22.1+ds2-1_arm64.deb ... 101s Unpacking libhts3t64:arm64 (1.22.1+ds2-1) ... 101s Selecting previously unselected package liblzf1:arm64. 101s Preparing to unpack .../11-liblzf1_3.6-4build1_arm64.deb ... 101s Unpacking liblzf1:arm64 (3.6-4build1) ... 101s Selecting previously unselected package libqhull-r8.0:arm64. 101s Preparing to unpack .../12-libqhull-r8.0_2020.2-8_arm64.deb ... 101s Unpacking libqhull-r8.0:arm64 (2020.2-8) ... 101s Selecting previously unselected package python3-h5py-serial. 101s Preparing to unpack .../13-python3-h5py-serial_3.15.1-4_arm64.deb ... 101s Unpacking python3-h5py-serial (3.15.1-4) ... 101s Selecting previously unselected package python3-h5py. 101s Preparing to unpack .../14-python3-h5py_3.15.1-4_all.deb ... 101s Unpacking python3-h5py (3.15.1-4) ... 101s Selecting previously unselected package python3-pytz. 101s Preparing to unpack .../15-python3-pytz_2025.2-5_all.deb ... 101s Unpacking python3-pytz (2025.2-5) ... 101s Selecting previously unselected package python3-pandas-lib:arm64. 101s Preparing to unpack .../16-python3-pandas-lib_2.3.3+dfsg-3_arm64.deb ... 101s Unpacking python3-pandas-lib:arm64 (2.3.3+dfsg-3) ... 101s Selecting previously unselected package python3-pandas. 101s Preparing to unpack .../17-python3-pandas_2.3.3+dfsg-3_all.deb ... 101s Unpacking python3-pandas (2.3.3+dfsg-3) ... 101s Selecting previously unselected package python3-decorator. 101s Preparing to unpack .../18-python3-decorator_5.2.1-2_all.deb ... 101s Unpacking python3-decorator (5.2.1-2) ... 101s Selecting previously unselected package python3-fastjsonschema. 102s Preparing to unpack .../19-python3-fastjsonschema_2.21.1-1_all.deb ... 102s Unpacking python3-fastjsonschema (2.21.1-1) ... 102s Selecting previously unselected package python3-platformdirs. 102s Preparing to unpack .../20-python3-platformdirs_4.5.1-1_all.deb ... 102s Unpacking python3-platformdirs (4.5.1-1) ... 102s Selecting previously unselected package python3-traitlets. 102s Preparing to unpack .../21-python3-traitlets_5.14.3+really5.14.3-2_all.deb ... 102s Unpacking python3-traitlets (5.14.3+really5.14.3-2) ... 102s Selecting previously unselected package python3-jupyter-core. 102s Preparing to unpack .../22-python3-jupyter-core_5.9.1-1_all.deb ... 102s Unpacking python3-jupyter-core (5.9.1-1) ... 102s Selecting previously unselected package python3-nbformat. 102s Preparing to unpack .../23-python3-nbformat_5.10.4-1_all.deb ... 102s Unpacking python3-nbformat (5.10.4-1) ... 102s Selecting previously unselected package python3-tenacity. 102s Preparing to unpack .../24-python3-tenacity_9.0.0-0ubuntu1_all.deb ... 102s Unpacking python3-tenacity (9.0.0-0ubuntu1) ... 102s Selecting previously unselected package python3-plotly. 102s Preparing to unpack .../25-python3-plotly_5.20.0+dfsg-1.1_all.deb ... 102s Unpacking python3-plotly (5.20.0+dfsg-1.1) ... 103s Selecting previously unselected package python3-pysam. 103s Preparing to unpack .../26-python3-pysam_0.23.3+ds-2_arm64.deb ... 103s Unpacking python3-pysam (0.23.3+ds-2) ... 103s Selecting previously unselected package python3-scipy. 103s Preparing to unpack .../27-python3-scipy_1.16.3-4_arm64.deb ... 103s Unpacking python3-scipy (1.16.3-4) ... 103s Selecting previously unselected package python3-tqdm. 103s Preparing to unpack .../28-python3-tqdm_4.67.3-1_all.deb ... 103s Unpacking python3-tqdm (4.67.3-1) ... 103s Selecting previously unselected package pycoqc. 103s Preparing to unpack .../29-pycoqc_2.5.2+dfsg-4_all.deb ... 103s Unpacking pycoqc (2.5.2+dfsg-4) ... 104s Setting up libhtscodecs2:arm64 (1.6.1-2build1) ... 104s Setting up python3-tenacity (9.0.0-0ubuntu1) ... 104s Setting up python3-tqdm (4.67.3-1) ... 104s Setting up libdeflate0:arm64 (1.23-2) ... 104s Setting up libqhull-r8.0:arm64 (2020.2-8) ... 104s Setting up python3-pytz (2025.2-5) ... 104s Setting up python3-platformdirs (4.5.1-1) ... 104s Setting up python3-decorator (5.2.1-2) ... 104s Setting up libblas3:arm64 (3.12.1-7ubuntu1) ... 104s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 104s Setting up liblzf1:arm64 (3.6-4build1) ... 104s Setting up python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 104s Setting up libgfortran5:arm64 (15.2.0-12ubuntu1) ... 104s Setting up python3-fastjsonschema (2.21.1-1) ... 104s Setting up python3-traitlets (5.14.3+really5.14.3-2) ... 105s Setting up libhts3t64:arm64 (1.22.1+ds2-1) ... 105s Setting up python3-jupyter-core (5.9.1-1) ... 105s Setting up libsz2:arm64 (1.1.5-1) ... 105s Setting up liblapack3:arm64 (3.12.1-7ubuntu1) ... 105s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 105s Setting up python3-pysam (0.23.3+ds-2) ... 105s Setting up python3-nbformat (5.10.4-1) ... 105s Setting up python3-plotly (5.20.0+dfsg-1.1) ... 111s Setting up python3-numpy (1:2.3.5+ds-3) ... 113s Setting up libhdf5-310:arm64 (1.14.6+repack-2) ... 113s Setting up libhdf5-hl-310:arm64 (1.14.6+repack-2) ... 113s Setting up python3-scipy (1.16.3-4) ... 117s Setting up python3-pandas-lib:arm64 (2.3.3+dfsg-3) ... 117s Setting up python3-h5py-serial (3.15.1-4) ... 117s Setting up python3-pandas (2.3.3+dfsg-3) ... 121s Setting up python3-h5py (3.15.1-4) ... 122s Setting up pycoqc (2.5.2+dfsg-4) ... 122s Processing triggers for libc-bin (2.42-2ubuntu4) ... 122s Processing triggers for man-db (2.13.1-1) ... 127s autopkgtest [17:32:18]: test run-unit-test: [----------------------- 129s Test 1 130s Checking arguments values 130s Check input data files 130s Parse data files 130s Merge data 130s Cleaning data 130s Loading plotting interface 131s PASS 131s 131s Test 2 131s Checking arguments values 131s Check input data files 131s Parse data files 131s Merge data 131s Cleaning data 131s Loading plotting interface 132s PASS 132s 132s Test 3 133s Checking arguments values 133s Check input data files 133s Parse data files 133s Merge data 133s Cleaning data 133s Loading plotting interface 134s PASS 134s 134s Test 4 134s Checking arguments values 134s Check input data files 134s Parse data files 137s Merge data 137s Cleaning data 137s PASS 137s 137s Test 5 137s Loading plotting interface 137s Checking arguments values 137s Check input data files 137s Parse data files 137s Merge data 137s Cleaning data 137s Loading plotting interface 137s PASS 137s 137s Test 6 138s PASS 138s 138s Test 7 139s Checking arguments values 139s Check input data files 139s Parse data files 139s Merge data 139s Cleaning data 139s Loading plotting interface 139s PASS 139s 139s Test 8 140s 0 reads [00:00, ? reads/s] 22 reads [00:00, 912.39 reads/s] 140s Total reads: 22 / Average speed: 520.28 reads/s 140s 140s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template 140s 37dfa1d5-5d84-486c-bf47-9eb6438f5645 40ebe55356ada6c830fa793745ef4c498d896c73 410 30 555 8.219 filtered_out 140s 9a1c5296-2ab1-4abd-8d50-e059754cf332 40ebe55356ada6c830fa793745ef4c498d896c73 319 33 1235 8.119 filtered_out 140s ed05c5e6-7aab-4970-a431-3411047764a6 40ebe55356ada6c830fa793745ef4c498d896c73 224 34 880 8.891 filtered_out 140s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out 140s f8325de9-a77e-4616-a4a8-69ecf32e1688 40ebe55356ada6c830fa793745ef4c498d896c73 354 16 568 8.206 filtered_out 140s 4e21bf07-e2df-42d8-b347-59ef2c0618ea 40ebe55356ada6c830fa793745ef4c498d896c73 290 31 1160 8.741 filtered_out 140s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out 140s 1f83ee80-ac29-46be-b8bc-9dc9325f1fa7 40ebe55356ada6c830fa793745ef4c498d896c73 382 35 819 7.414 filtered_out 140s 97205d42-93ac-4c99-af78-e553f7d1ff83 40ebe55356ada6c830fa793745ef4c498d896c73 343 26 1584 8.987 filtered_out 140s PASS 140s 140s Test 9 141s Check input data and options 141s Start processing fast5 files 141s 0 reads [00:00, ? reads/s] 22 reads [00:00, 1314.90 reads/s] 141s Overall counts valid files: 22 141s 141s fields found mean_qscore_template: 22 141s called_events: 22 141s duration: 22 141s strand_score: 22 141s 141s fields not found 141s Total reads: 22 / Average speed: 355.17 reads/s 141s 141s mean_qscore_template called_events duration strand_score 141s 8.219 2080 31208 -0.0011 141s 8.119 3181 47720 -0.0004 141s 7.805 1438 21583 -0.0006 141s 8.891 2774 41612 -0.0006 141s 8.206 1649 24747 -0.0009 141s 8.741 3117 46767 -0.0006 141s 8.56 5838 87570 -0.0003 141s 8.234 1827 27409 -0.0011 141s 7.414 3017 45267 -0.0002 141s PASS 141s 141s Test 10 142s Check input data and options 142s Start processing fast5 files 142s 0 reads [00:00, ? reads/s] 22 reads [00:00, 1034.20 reads/s] 142s Overall counts valid files: 22 142s 142s fields found read_id: 22 142s run_id: 22 142s channel: 22 142s start_time: 22 142s sequence_length_template: 22 142s mean_qscore_template: 22 142s calibration_strand_genome_template: 22 142s 142s fields not found barcode_arrangement: 22 142s 142s Total reads: 22 / Average speed: 506.56 reads/s 142s 142s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template path 142s 37dfa1d5-5d84-486c-bf47-9eb6438f5645 40ebe55356ada6c830fa793745ef4c498d896c73 410 30 555 8.219 filtered_out /tmp/autopkgtest.EjjVQf/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_410_strand.fast5 142s 9a1c5296-2ab1-4abd-8d50-e059754cf332 40ebe55356ada6c830fa793745ef4c498d896c73 319 33 1235 8.119 filtered_out /tmp/autopkgtest.EjjVQf/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_319_strand.fast5 142s ed05c5e6-7aab-4970-a431-3411047764a6 40ebe55356ada6c830fa793745ef4c498d896c73 224 34 880 8.891 filtered_out /tmp/autopkgtest.EjjVQf/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_224_strand.fast5 142s f8325de9-a77e-4616-a4a8-69ecf32e1688 40ebe55356ada6c830fa793745ef4c498d896c73 354 16 568 8.206 filtered_out /tmp/autopkgtest.EjjVQf/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_354_strand.fast5 142s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out /tmp/autopkgtest.EjjVQf/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_103_strand.fast5 142s 4e21bf07-e2df-42d8-b347-59ef2c0618ea 40ebe55356ada6c830fa793745ef4c498d896c73 290 31 1160 8.741 filtered_out /tmp/autopkgtest.EjjVQf/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_290_strand.fast5 142s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out /tmp/autopkgtest.EjjVQf/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_121_strand.fast5 142s 1f83ee80-ac29-46be-b8bc-9dc9325f1fa7 40ebe55356ada6c830fa793745ef4c498d896c73 382 35 819 7.414 filtered_out /tmp/autopkgtest.EjjVQf/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_382_strand.fast5 142s 97205d42-93ac-4c99-af78-e553f7d1ff83 40ebe55356ada6c830fa793745ef4c498d896c73 343 26 1584 8.987 filtered_out /tmp/autopkgtest.EjjVQf/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_343_strand.fast5 142s PASS 142s 142s Test 11 143s Import data from sequencing summary file(s) and cleanup 143s Read files and import in a dataframe 143s Check input data files 143s Parse data files 143s Merge data 143s Cleanup missing barcodes values 143s Cleaning up low frequency barcodes 143s Split data per barcode 144s Processing data for Barcode barcode02 144s Processing data for Barcode barcode07 144s Processing data for Barcode barcode08 144s Processing data for Barcode barcode09 144s Processing data for Barcode barcode10 144s Processing data for Barcode barcode11 144s Processing data for Barcode barcode12 144s Processing data for Barcode unclassified 144s Barcode Counts 144s Counts Write 144s barcode02 2 False 144s barcode07 1 False 144s barcode08 30 False 144s barcode09 9945 True 144s barcode10 12644 True 144s barcode11 13594 True 144s barcode12 9813 True 144s unclassified 3971 False 145s PASS 145s 145s Test 12 145s General info 145s package_name: pycoQC 145s package_version: 2.5.2 145s timestamp: 2026-02-05 17:32:36.613367 145s 145s Runtime options 145s summary_file: ['Guppy-basecall-1D-DNA_sequencing_summary.txt'] 145s barcode_file: ['Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt'] 145s output_dir: results/ 145s output_unclassified: False 145s min_barcode_percent: 0.1 145s verbose: True 145s quiet: False 145s 145s Import data from sequencing summary file(s) and cleanup 145s Read files and import in a dataframe 145s Check input data files 145s Sequencing summary files found: Guppy-basecall-1D-DNA_sequencing_summary.txt 145s Barcode files found: Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt 145s Parse data files 145s Parse summary files 145s 3,999 reads found in initial file 145s Parse barcode files 145s Found valid Deepbinner barcode file 145s 3,775 reads with barcodes assigned 145s Merge data 145s Cleanup missing barcodes values 145s Cleaning up low frequency barcodes 145s Split data per barcode 145s Processing data for Barcode 1 145s Processing data for Barcode 2 145s Processing data for Barcode 3 145s Processing data for Barcode 4 145s Processing data for Barcode 5 145s Processing data for Barcode 6 145s Processing data for Barcode 7 145s Processing data for Barcode 8 145s Processing data for Barcode unclassified 145s Barcode Counts 145s Counts Write 145s 1 534 True 145s 2 206 True 145s 3 562 True 145s 4 579 True 145s 5 590 True 145s 6 655 True 145s 7 271 True 145s 8 378 True 145s unclassified 224 False 146s PASS 146s 146s Check if files really exist 146s PASS 146s 146s autopkgtest [17:32:37]: test run-unit-test: -----------------------] 146s autopkgtest [17:32:37]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 146s run-unit-test PASS 151s autopkgtest [17:32:42]: @@@@@@@@@@@@@@@@@@@@ summary 151s run-unit-test PASS