0s autopkgtest [16:33:23]: starting date and time: 2026-02-05 16:33:23+0000 0s autopkgtest [16:33:23]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [16:33:23]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.q46h4dw8/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.221 lxd-armhf-10.145.243.221:autopkgtest/ubuntu/resolute/armhf 25s autopkgtest [16:33:48]: testbed dpkg architecture: armhf 26s autopkgtest [16:33:49]: testbed apt version: 3.1.14 30s autopkgtest [16:33:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 32s autopkgtest [16:33:55]: testbed release detected to be: None 40s autopkgtest [16:34:03]: updating testbed package index (apt update) 42s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 43s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 43s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 43s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 43s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [230 kB] 44s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [36.0 kB] 44s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 44s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1686 kB] 47s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [256 kB] 47s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1372 kB] 51s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [10.3 kB] 51s Get:12 http://ftpmaster.internal/ubuntu resolute/main Sources [1399 kB] 53s Get:13 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.3 MB] 83s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1374 kB] 84s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.3 MB] 99s Fetched 43.4 MB in 57s (763 kB/s) 100s Reading package lists... 106s autopkgtest [16:35:09]: upgrading testbed (apt dist-upgrade and autopurge) 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Calculating upgrade... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Solving dependencies... 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s autopkgtest [16:35:17]: rebooting testbed after setup commands that affected boot 154s autopkgtest [16:35:57]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 179s autopkgtest [16:36:22]: @@@@@@@@@@@@@@@@@@@@ apt-source pycoqc 257s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (dsc) [2027 B] 257s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (tar) [41.6 MB] 257s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (diff) [6840 B] 257s gpgv: Signature made Sat Jan 18 02:09:23 2025 UTC 257s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 257s gpgv: issuer "tchet@debian.org" 257s gpgv: Can't check signature: No public key 257s dpkg-source: warning: cannot verify inline signature for ./pycoqc_2.5.2+dfsg-4.dsc: no acceptable signature found 259s autopkgtest [16:37:42]: testing package pycoqc version 2.5.2+dfsg-4 261s autopkgtest [16:37:44]: build not needed 280s autopkgtest [16:38:03]: test run-unit-test: preparing testbed 282s Reading package lists... 283s Building dependency tree... 283s Reading state information... 283s Solving dependencies... 283s The following NEW packages will be installed: 283s libblas3 libdeflate0 libgfortran5 libhdf5-310 libhdf5-hl-310 libhts3t64 283s libhtscodecs2 liblapack3 liblzf1 libqhull-r8.0 libsz2 pycoqc 283s python3-decorator python3-fastjsonschema python3-h5py python3-h5py-serial 283s python3-jupyter-core python3-nbformat python3-numpy python3-numpy-dev 283s python3-pandas python3-pandas-lib python3-platformdirs python3-plotly 283s python3-pysam python3-pytz python3-scipy python3-tenacity python3-tqdm 283s python3-traitlets 283s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 283s Need to get 47.0 MB of archives. 283s After this operation, 276 MB of additional disk space will be used. 283s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy-dev armhf 1:2.3.5+ds-3 [141 kB] 284s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 284s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-12ubuntu1 [334 kB] 285s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7ubuntu1 [2090 kB] 288s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy armhf 1:2.3.5+ds-3 [4729 kB] 295s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2 [38.7 kB] 295s Get:7 http://ftpmaster.internal/ubuntu resolute/universe armhf libsz2 armhf 1.1.5-1 [16.3 kB] 295s Get:8 http://ftpmaster.internal/ubuntu resolute/universe armhf libhdf5-310 armhf 1.14.6+repack-2 [1423 kB] 297s Get:9 http://ftpmaster.internal/ubuntu resolute/universe armhf libhdf5-hl-310 armhf 1.14.6+repack-2 [58.9 kB] 297s Get:10 http://ftpmaster.internal/ubuntu resolute/universe armhf libhtscodecs2 armhf 1.6.1-2build1 [67.0 kB] 297s Get:11 http://ftpmaster.internal/ubuntu resolute/universe armhf libhts3t64 armhf 1.22.1+ds2-1 [408 kB] 298s Get:12 http://ftpmaster.internal/ubuntu resolute/universe armhf liblzf1 armhf 3.6-4build1 [6592 B] 298s Get:13 http://ftpmaster.internal/ubuntu resolute/universe armhf libqhull-r8.0 armhf 2020.2-8 [175 kB] 298s Get:14 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-h5py-serial armhf 3.15.1-4 [1562 kB] 300s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-h5py all 3.15.1-4 [11.3 kB] 300s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pytz all 2025.2-5 [32.4 kB] 300s Get:17 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pandas-lib armhf 2.3.3+dfsg-3 [7022 kB] 311s Get:18 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pandas all 2.3.3+dfsg-3 [2948 kB] 315s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf python3-decorator all 5.2.1-2 [28.1 kB] 315s Get:20 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-fastjsonschema all 2.21.1-1 [20.4 kB] 315s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf python3-platformdirs all 4.5.1-1 [17.1 kB] 315s Get:22 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-traitlets all 5.14.3+really5.14.3-2 [71.7 kB] 315s Get:23 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-jupyter-core all 5.9.1-1 [28.9 kB] 315s Get:24 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-nbformat all 5.10.4-1 [39.2 kB] 315s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf python3-tenacity all 9.0.0-0ubuntu1 [17.0 kB] 315s Get:26 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-plotly all 5.20.0+dfsg-1.1 [2766 kB] 320s Get:27 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pysam armhf 0.23.3+ds-2 [4358 kB] 327s Get:28 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-scipy armhf 1.16.3-4 [18.3 MB] 345s Get:29 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf python3-tqdm all 4.67.3-1 [93.3 kB] 345s Get:30 http://ftpmaster.internal/ubuntu resolute/universe armhf pycoqc all 2.5.2+dfsg-4 [36.4 kB] 345s Fetched 47.0 MB in 1min 1s (764 kB/s) 345s Selecting previously unselected package python3-numpy-dev:armhf. 346s (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 ... 68395 files and directories currently installed.) 346s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_armhf.deb ... 346s Unpacking python3-numpy-dev:armhf (1:2.3.5+ds-3) ... 346s Selecting previously unselected package libblas3:armhf. 346s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_armhf.deb ... 346s Unpacking libblas3:armhf (3.12.1-7ubuntu1) ... 346s Selecting previously unselected package libgfortran5:armhf. 346s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_armhf.deb ... 346s Unpacking libgfortran5:armhf (15.2.0-12ubuntu1) ... 346s Selecting previously unselected package liblapack3:armhf. 346s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_armhf.deb ... 346s Unpacking liblapack3:armhf (3.12.1-7ubuntu1) ... 346s Selecting previously unselected package python3-numpy. 346s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_armhf.deb ... 346s Unpacking python3-numpy (1:2.3.5+ds-3) ... 346s Selecting previously unselected package libdeflate0:armhf. 346s Preparing to unpack .../05-libdeflate0_1.23-2_armhf.deb ... 346s Unpacking libdeflate0:armhf (1.23-2) ... 346s Selecting previously unselected package libsz2:armhf. 346s Preparing to unpack .../06-libsz2_1.1.5-1_armhf.deb ... 346s Unpacking libsz2:armhf (1.1.5-1) ... 346s Selecting previously unselected package libhdf5-310:armhf. 346s Preparing to unpack .../07-libhdf5-310_1.14.6+repack-2_armhf.deb ... 346s Unpacking libhdf5-310:armhf (1.14.6+repack-2) ... 346s Selecting previously unselected package libhdf5-hl-310:armhf. 346s Preparing to unpack .../08-libhdf5-hl-310_1.14.6+repack-2_armhf.deb ... 346s Unpacking libhdf5-hl-310:armhf (1.14.6+repack-2) ... 346s Selecting previously unselected package libhtscodecs2:armhf. 346s Preparing to unpack .../09-libhtscodecs2_1.6.1-2build1_armhf.deb ... 346s Unpacking libhtscodecs2:armhf (1.6.1-2build1) ... 346s Selecting previously unselected package libhts3t64:armhf. 346s Preparing to unpack .../10-libhts3t64_1.22.1+ds2-1_armhf.deb ... 346s Unpacking libhts3t64:armhf (1.22.1+ds2-1) ... 346s Selecting previously unselected package liblzf1:armhf. 346s Preparing to unpack .../11-liblzf1_3.6-4build1_armhf.deb ... 346s Unpacking liblzf1:armhf (3.6-4build1) ... 346s Selecting previously unselected package libqhull-r8.0:armhf. 346s Preparing to unpack .../12-libqhull-r8.0_2020.2-8_armhf.deb ... 346s Unpacking libqhull-r8.0:armhf (2020.2-8) ... 346s Selecting previously unselected package python3-h5py-serial. 346s Preparing to unpack .../13-python3-h5py-serial_3.15.1-4_armhf.deb ... 346s Unpacking python3-h5py-serial (3.15.1-4) ... 346s Selecting previously unselected package python3-h5py. 346s Preparing to unpack .../14-python3-h5py_3.15.1-4_all.deb ... 346s Unpacking python3-h5py (3.15.1-4) ... 346s Selecting previously unselected package python3-pytz. 347s Preparing to unpack .../15-python3-pytz_2025.2-5_all.deb ... 347s Unpacking python3-pytz (2025.2-5) ... 347s Selecting previously unselected package python3-pandas-lib:armhf. 347s Preparing to unpack .../16-python3-pandas-lib_2.3.3+dfsg-3_armhf.deb ... 347s Unpacking python3-pandas-lib:armhf (2.3.3+dfsg-3) ... 347s Selecting previously unselected package python3-pandas. 347s Preparing to unpack .../17-python3-pandas_2.3.3+dfsg-3_all.deb ... 347s Unpacking python3-pandas (2.3.3+dfsg-3) ... 347s Selecting previously unselected package python3-decorator. 347s Preparing to unpack .../18-python3-decorator_5.2.1-2_all.deb ... 347s Unpacking python3-decorator (5.2.1-2) ... 347s Selecting previously unselected package python3-fastjsonschema. 347s Preparing to unpack .../19-python3-fastjsonschema_2.21.1-1_all.deb ... 347s Unpacking python3-fastjsonschema (2.21.1-1) ... 347s Selecting previously unselected package python3-platformdirs. 347s Preparing to unpack .../20-python3-platformdirs_4.5.1-1_all.deb ... 347s Unpacking python3-platformdirs (4.5.1-1) ... 347s Selecting previously unselected package python3-traitlets. 347s Preparing to unpack .../21-python3-traitlets_5.14.3+really5.14.3-2_all.deb ... 347s Unpacking python3-traitlets (5.14.3+really5.14.3-2) ... 347s Selecting previously unselected package python3-jupyter-core. 347s Preparing to unpack .../22-python3-jupyter-core_5.9.1-1_all.deb ... 347s Unpacking python3-jupyter-core (5.9.1-1) ... 347s Selecting previously unselected package python3-nbformat. 347s Preparing to unpack .../23-python3-nbformat_5.10.4-1_all.deb ... 347s Unpacking python3-nbformat (5.10.4-1) ... 348s Selecting previously unselected package python3-tenacity. 348s Preparing to unpack .../24-python3-tenacity_9.0.0-0ubuntu1_all.deb ... 348s Unpacking python3-tenacity (9.0.0-0ubuntu1) ... 348s Selecting previously unselected package python3-plotly. 348s Preparing to unpack .../25-python3-plotly_5.20.0+dfsg-1.1_all.deb ... 348s Unpacking python3-plotly (5.20.0+dfsg-1.1) ... 350s Selecting previously unselected package python3-pysam. 350s Preparing to unpack .../26-python3-pysam_0.23.3+ds-2_armhf.deb ... 350s Unpacking python3-pysam (0.23.3+ds-2) ... 350s Selecting previously unselected package python3-scipy. 350s Preparing to unpack .../27-python3-scipy_1.16.3-4_armhf.deb ... 350s Unpacking python3-scipy (1.16.3-4) ... 350s Selecting previously unselected package python3-tqdm. 350s Preparing to unpack .../28-python3-tqdm_4.67.3-1_all.deb ... 350s Unpacking python3-tqdm (4.67.3-1) ... 351s Selecting previously unselected package pycoqc. 351s Preparing to unpack .../29-pycoqc_2.5.2+dfsg-4_all.deb ... 351s Unpacking pycoqc (2.5.2+dfsg-4) ... 351s Setting up libhtscodecs2:armhf (1.6.1-2build1) ... 351s Setting up python3-tenacity (9.0.0-0ubuntu1) ... 351s Setting up python3-tqdm (4.67.3-1) ... 351s Setting up libdeflate0:armhf (1.23-2) ... 351s Setting up libqhull-r8.0:armhf (2020.2-8) ... 351s Setting up python3-pytz (2025.2-5) ... 351s Setting up python3-platformdirs (4.5.1-1) ... 352s Setting up python3-decorator (5.2.1-2) ... 352s Setting up libblas3:armhf (3.12.1-7ubuntu1) ... 352s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 352s Setting up liblzf1:armhf (3.6-4build1) ... 352s Setting up python3-numpy-dev:armhf (1:2.3.5+ds-3) ... 352s Setting up libgfortran5:armhf (15.2.0-12ubuntu1) ... 352s Setting up python3-fastjsonschema (2.21.1-1) ... 352s Setting up python3-traitlets (5.14.3+really5.14.3-2) ... 352s Setting up libhts3t64:armhf (1.22.1+ds2-1) ... 352s Setting up python3-jupyter-core (5.9.1-1) ... 352s Setting up libsz2:armhf (1.1.5-1) ... 352s Setting up liblapack3:armhf (3.12.1-7ubuntu1) ... 352s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 352s Setting up python3-pysam (0.23.3+ds-2) ... 353s Setting up python3-nbformat (5.10.4-1) ... 353s Setting up python3-plotly (5.20.0+dfsg-1.1) ... 360s Setting up python3-numpy (1:2.3.5+ds-3) ... 362s Setting up libhdf5-310:armhf (1.14.6+repack-2) ... 362s Setting up libhdf5-hl-310:armhf (1.14.6+repack-2) ... 362s Setting up python3-scipy (1.16.3-4) ... 366s Setting up python3-pandas-lib:armhf (2.3.3+dfsg-3) ... 366s Setting up python3-h5py-serial (3.15.1-4) ... 366s Setting up python3-pandas (2.3.3+dfsg-3) ... 371s Setting up python3-h5py (3.15.1-4) ... 371s Setting up pycoqc (2.5.2+dfsg-4) ... 372s Processing triggers for libc-bin (2.42-2ubuntu4) ... 372s Processing triggers for man-db (2.13.1-1) ... 381s autopkgtest [16:39:44]: test run-unit-test: [----------------------- 383s Test 1 384s Checking arguments values 384s Check input data files 384s Parse data files 384s Merge data 384s Cleaning data 384s Loading plotting interface 385s PASS 385s 385s Test 2 386s Checking arguments values 386s Check input data files 386s Parse data files 386s Merge data 386s Cleaning data 386s Loading plotting interface 387s PASS 387s 387s Test 3 388s Checking arguments values 388s Check input data files 388s Parse data files 388s Merge data 388s Cleaning data 388s Loading plotting interface 389s PASS 389s 389s Test 4 389s Checking arguments values 389s Check input data files 389s Parse data files 389s Merge data 389s Cleaning data 390s Loading plotting interface 391s PASS 391s 391s Test 5 391s Checking arguments values 391s Check input data files 391s Parse data files 391s Merge data 391s Cleaning data 391s Loading plotting interface 392s PASS 392s 392s Test 6 393s PASS 393s 393s Test 7 394s Checking arguments values 394s Check input data files 394s Parse data files 394s Merge data 394s Cleaning data 394s Loading plotting interface 395s PASS 395s 395s Test 8 396s 0 reads [00:00, ? reads/s] 22 reads [00:00, 383.02 reads/s] 396s Total reads: 22 / Average speed: 305.8 reads/s 396s 396s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template 396s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out 396s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out 396s c38cbad9-d91e-4208-9317-832f4e2cc289 40ebe55356ada6c830fa793745ef4c498d896c73 113 30 824 8.693 filtered_out 396s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out 396s 5b7fadd0-c646-4c7b-9800-66ee658a5ca8 40ebe55356ada6c830fa793745ef4c498d896c73 150 37 468 7.608 filtered_out 396s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out 396s bcb20156-a5fe-4daa-aad9-b62c286e468d 40ebe55356ada6c830fa793745ef4c498d896c73 192 21 306 7.337 filtered_out 396s ed05c5e6-7aab-4970-a431-3411047764a6 40ebe55356ada6c830fa793745ef4c498d896c73 224 34 880 8.891 filtered_out 396s 2c32553e-62c6-4c7a-bf05-249771364f04 40ebe55356ada6c830fa793745ef4c498d896c73 237 11 1151 8.544 filtered_out 396s PASS 396s 396s Test 9 396s Check input data and options 396s Start processing fast5 files 396s 0 reads [00:00, ? reads/s] 22 reads [00:00, 1563.39 reads/s] 396s Overall counts valid files: 22 396s 396s fields found mean_qscore_template: 22 396s called_events: 22 396s duration: 22 396s strand_score: 22 396s 396s fields not found 396s Total reads: 22 / Average speed: 759.26 reads/s 396s 397s mean_qscore_template called_events duration strand_score 397s 8.56 5838 87570 -0.0003 397s 8.693 2383 35752 -0.0005 397s 9.407 2848 42730 -0.0003 397s 7.805 1438 21583 -0.0006 397s 7.608 1615 24233 -0.0007 397s 8.23 2778 51387 -0.0007 397s 7.337 1972 29589 -0.0009 397s 8.54 2023 30405 -0.0003 397s 7.881 1513 24541 -0.0007 397s PASS 397s 397s Test 10 397s Check input data and options 397s Start processing fast5 files 397s 0 reads [00:00, ? reads/s] 22 reads [00:00, 1015.63 reads/s] 397s Overall counts valid files: 22 397s 397s fields found read_id: 22 397s run_id: 22 397s channel: 22 397s start_time: 22 397s sequence_length_template: 22 397s mean_qscore_template: 22 397s calibration_strand_genome_template: 22 397s 397s fields not found barcode_arrangement: 22 397s 397s Total reads: 22 / Average speed: 643.77 reads/s 397s 398s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template path 398s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out /tmp/autopkgtest.FPDc2h/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_103_strand.fast5 398s c38cbad9-d91e-4208-9317-832f4e2cc289 40ebe55356ada6c830fa793745ef4c498d896c73 113 30 824 8.693 filtered_out /tmp/autopkgtest.FPDc2h/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_113_strand.fast5 398s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out /tmp/autopkgtest.FPDc2h/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_108_strand.fast5 398s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out /tmp/autopkgtest.FPDc2h/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_121_strand.fast5 398s 5b7fadd0-c646-4c7b-9800-66ee658a5ca8 40ebe55356ada6c830fa793745ef4c498d896c73 150 37 468 7.608 filtered_out /tmp/autopkgtest.FPDc2h/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_150_strand.fast5 398s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out /tmp/autopkgtest.FPDc2h/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_191_strand.fast5 398s bcb20156-a5fe-4daa-aad9-b62c286e468d 40ebe55356ada6c830fa793745ef4c498d896c73 192 21 306 7.337 filtered_out /tmp/autopkgtest.FPDc2h/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_192_strand.fast5 398s ed05c5e6-7aab-4970-a431-3411047764a6 40ebe55356ada6c830fa793745ef4c498d896c73 224 34 880 8.891 filtered_out /tmp/autopkgtest.FPDc2h/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_224_strand.fast5 398s 2c32553e-62c6-4c7a-bf05-249771364f04 40ebe55356ada6c830fa793745ef4c498d896c73 237 11 1151 8.544 filtered_out /tmp/autopkgtest.FPDc2h/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_237_strand.fast5 398s PASS 398s 398s Test 11 398s Import data from sequencing summary file(s) and cleanup 398s Read files and import in a dataframe 398s Check input data files 398s Parse data files 399s Merge data 399s Cleanup missing barcodes values 399s Cleaning up low frequency barcodes 399s Split data per barcode 399s Processing data for Barcode barcode02 399s Processing data for Barcode barcode07 399s Processing data for Barcode barcode08 399s Processing data for Barcode barcode09 399s Processing data for Barcode barcode10 399s Processing data for Barcode barcode11 400s Processing data for Barcode barcode12 400s Processing data for Barcode unclassified 400s Barcode Counts 400s Counts Write 400s barcode02 2 False 400s barcode07 1 False 400s barcode08 30 False 400s barcode09 9945 True 400s barcode10 12644 True 400s barcode11 13594 True 400s barcode12 9813 True 400s unclassified 3971 False 400s PASS 400s 400s Test 12 401s General info 401s package_name: pycoQC 401s package_version: 2.5.2 401s timestamp: 2026-02-05 16:40:04.423971 401s 401s Runtime options 401s summary_file: ['Guppy-basecall-1D-DNA_sequencing_summary.txt'] 401s barcode_file: ['Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt'] 401s output_dir: results/ 401s output_unclassified: False 401s min_barcode_percent: 0.1 401s verbose: True 401s quiet: False 401s 401s Import data from sequencing summary file(s) and cleanup 401s Read files and import in a dataframe 401s Check input data files 401s Sequencing summary files found: Guppy-basecall-1D-DNA_sequencing_summary.txt 401s Barcode files found: Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt 401s Parse data files 401s Parse summary files 401s 3,999 reads found in initial file 401s Parse barcode files 401s Found valid Deepbinner barcode file 401s 3,775 reads with barcodes assigned 401s Merge data 401s Cleanup missing barcodes values 401s Cleaning up low frequency barcodes 401s Split data per barcode 401s Processing data for Barcode 1 401s Processing data for Barcode 2 401s Processing data for Barcode 3 401s Processing data for Barcode 4 401s Processing data for Barcode 5 401s Processing data for Barcode 6 401s Processing data for Barcode 7 401s Processing data for Barcode 8 401s Processing data for Barcode unclassified 401s Barcode Counts 401s Counts Write 401s 1 534 True 401s 2 206 True 401s 3 562 True 401s 4 579 True 401s 5 590 True 401s 6 655 True 401s 7 271 True 401s 8 378 True 401s unclassified 224 False 401s PASS 401s 401s Check if files really exist 401s PASS 401s 402s autopkgtest [16:40:05]: test run-unit-test: -----------------------] 406s autopkgtest [16:40:09]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 406s run-unit-test PASS 409s autopkgtest [16:40:12]: @@@@@@@@@@@@@@@@@@@@ summary 409s run-unit-test PASS