0s autopkgtest [18:08:22]: starting date and time: 2026-02-03 18:08:22+0000 0s autopkgtest [18:08:22]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [18:08:22]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.o5cg6xr5/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:jinja2 --apt-upgrade pycoqc --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=jinja2/3.1.6-1build1 -- 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-arm64-2.secgroup --name adt-resolute-arm64-pycoqc-20260203-180822-juju-7f2275-prod-proposed-migration-environment-2-98f37fd2-2cac-4053-b6ca-12381fe021e7 --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/ 3s Creating nova instance adt-resolute-arm64-pycoqc-20260203-180822-juju-7f2275-prod-proposed-migration-environment-2-98f37fd2-2cac-4053-b6ca-12381fe021e7 from image adt/ubuntu-resolute-arm64-server-20260203.img (UUID fd4bac28-a946-4216-8755-72db0faf84da)... 53s autopkgtest [18:09:15]: testbed dpkg architecture: arm64 53s autopkgtest [18:09:15]: testbed apt version: 3.1.14 53s autopkgtest [18:09:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 53s autopkgtest [18:09:15]: testbed release detected to be: None 54s autopkgtest [18:09:16]: updating testbed package index (apt update) 54s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 54s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 54s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 54s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 54s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1327 kB] 55s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [241 kB] 55s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [27.9 kB] 55s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 55s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [297 kB] 55s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [6940 B] 55s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [52.9 kB] 55s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [328 B] 55s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1184 kB] 55s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [27.9 kB] 55s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [21.5 kB] 55s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [744 B] 58s Fetched 3317 kB in 1s (3689 kB/s) 58s Reading package lists... 60s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 60s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 60s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 60s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 61s Reading package lists... 61s Reading package lists... 61s Building dependency tree... 61s Reading state information... 62s Calculating upgrade... 62s The following packages will be upgraded: 62s firmware-sof-signed mtd-utils powermgmt-base python3-jinja2 62s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 62s Need to get 2279 kB of archives. 62s After this operation, 2048 B of additional disk space will be used. 62s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 firmware-sof-signed all 2025.05.1-1build1 [1696 kB] 62s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 powermgmt-base all 1.38ubuntu2 [7878 B] 62s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-jinja2 all 3.1.6-1build1 [109 kB] 62s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 mtd-utils arm64 1:2.3.0-1ubuntu2 [466 kB] 63s dpkg-preconfigure: unable to re-open stdin: No such file or directory 63s Fetched 2279 kB in 0s (6757 kB/s) 63s (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.) 63s Preparing to unpack .../firmware-sof-signed_2025.05.1-1build1_all.deb ... 63s Unpacking firmware-sof-signed (2025.05.1-1build1) over (2025.05.1-1) ... 63s Preparing to unpack .../powermgmt-base_1.38ubuntu2_all.deb ... 63s Unpacking powermgmt-base (1.38ubuntu2) over (1.38ubuntu1) ... 63s Preparing to unpack .../python3-jinja2_3.1.6-1build1_all.deb ... 63s Unpacking python3-jinja2 (3.1.6-1build1) over (3.1.6-1) ... 63s Preparing to unpack .../mtd-utils_1%3a2.3.0-1ubuntu2_arm64.deb ... 63s Unpacking mtd-utils (1:2.3.0-1ubuntu2) over (1:2.3.0-1ubuntu1) ... 63s Setting up powermgmt-base (1.38ubuntu2) ... 63s Setting up firmware-sof-signed (2025.05.1-1build1) ... 64s Setting up mtd-utils (1:2.3.0-1ubuntu2) ... 64s Setting up python3-jinja2 (3.1.6-1build1) ... 64s Processing triggers for man-db (2.13.1-1) ... 65s autopkgtest [18:09:27]: upgrading testbed (apt dist-upgrade and autopurge) 65s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s Calculating upgrade... 66s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s Solving dependencies... 67s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 69s autopkgtest [18:09:31]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:41:39 UTC 2026 69s autopkgtest [18:09:31]: @@@@@@@@@@@@@@@@@@@@ apt-source pycoqc 72s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (dsc) [2027 B] 72s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (tar) [41.6 MB] 72s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (diff) [6840 B] 72s gpgv: Signature made Sat Jan 18 02:09:23 2025 UTC 72s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 72s gpgv: issuer "tchet@debian.org" 72s gpgv: Can't check signature: No public key 72s dpkg-source: warning: cannot verify inline signature for ./pycoqc_2.5.2+dfsg-4.dsc: no acceptable signature found 74s autopkgtest [18:09:36]: testing package pycoqc version 2.5.2+dfsg-4 74s autopkgtest [18:09:36]: build not needed 78s autopkgtest [18:09:40]: test run-unit-test: preparing testbed 78s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s Solving dependencies... 79s The following NEW packages will be installed: 79s libblas3 libdeflate0 libgfortran5 libhdf5-310 libhdf5-hl-310 libhts3t64 79s libhtscodecs2 liblapack3 liblzf1 libqhull-r8.0 libsz2 pycoqc 79s python3-decorator python3-fastjsonschema python3-h5py python3-h5py-serial 79s python3-jupyter-core python3-nbformat python3-numpy python3-numpy-dev 79s python3-pandas python3-pandas-lib python3-platformdirs python3-plotly 79s python3-pysam python3-pytz python3-scipy python3-tenacity python3-tqdm 79s python3-traitlets 79s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 79s Need to get 45.7 MB of archives. 79s After this operation, 314 MB of additional disk space will be used. 79s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.3.5+ds-3 [366 kB] 79s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 79s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 79s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 80s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.3.5+ds-3 [4569 kB] 80s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 80s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 libsz2 arm64 1.1.5-1 [17.0 kB] 80s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-310 arm64 1.14.6+repack-2 [1287 kB] 80s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-hl-310 arm64 1.14.6+repack-2 [59.1 kB] 80s Get:10 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2build1 [83.8 kB] 80s Get:11 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhts3t64 arm64 1.22.1+ds2-1 [442 kB] 80s Get:12 http://ftpmaster.internal/ubuntu resolute/universe arm64 liblzf1 arm64 3.6-4build1 [7330 B] 80s Get:13 http://ftpmaster.internal/ubuntu resolute/universe arm64 libqhull-r8.0 arm64 2020.2-8 [191 kB] 80s Get:14 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-h5py-serial arm64 3.15.1-4 [1483 kB] 80s Get:15 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-h5py all 3.15.1-4 [11.3 kB] 80s Get:16 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytz all 2025.2-5 [32.4 kB] 80s Get:17 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.3.3+dfsg-3 [6290 kB] 81s Get:18 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.3.3+dfsg-3 [2948 kB] 81s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-decorator all 5.2.1-2 [28.1 kB] 81s Get:20 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fastjsonschema all 2.21.1-1 [20.4 kB] 81s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-platformdirs all 4.5.1-1 [17.1 kB] 81s Get:22 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-traitlets all 5.14.3+really5.14.3-2 [71.7 kB] 81s Get:23 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-jupyter-core all 5.9.1-1 [28.9 kB] 81s Get:24 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-nbformat all 5.10.4-1 [39.2 kB] 81s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-tenacity all 9.0.0-0ubuntu1 [17.0 kB] 81s Get:26 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-plotly all 5.20.0+dfsg-1.1 [2766 kB] 81s Get:27 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pysam arm64 0.23.3+ds-2 [4348 kB] 81s Get:28 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-scipy arm64 1.16.3-4 [17.5 MB] 82s Get:29 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-tqdm all 4.67.1-7 [93.3 kB] 82s Get:30 http://ftpmaster.internal/ubuntu resolute/universe arm64 pycoqc all 2.5.2+dfsg-4 [36.4 kB] 82s Fetched 45.7 MB in 2s (18.9 MB/s) 82s Selecting previously unselected package python3-numpy-dev:arm64. 82s (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.) 82s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_arm64.deb ... 82s Unpacking python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 82s Selecting previously unselected package libblas3:arm64. 82s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_arm64.deb ... 82s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 82s Selecting previously unselected package libgfortran5:arm64. 82s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_arm64.deb ... 82s Unpacking libgfortran5:arm64 (15.2.0-12ubuntu1) ... 82s Selecting previously unselected package liblapack3:arm64. 82s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 82s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 82s Selecting previously unselected package python3-numpy. 82s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_arm64.deb ... 82s Unpacking python3-numpy (1:2.3.5+ds-3) ... 82s Selecting previously unselected package libdeflate0:arm64. 82s Preparing to unpack .../05-libdeflate0_1.23-2_arm64.deb ... 82s Unpacking libdeflate0:arm64 (1.23-2) ... 82s Selecting previously unselected package libsz2:arm64. 82s Preparing to unpack .../06-libsz2_1.1.5-1_arm64.deb ... 82s Unpacking libsz2:arm64 (1.1.5-1) ... 82s Selecting previously unselected package libhdf5-310:arm64. 82s Preparing to unpack .../07-libhdf5-310_1.14.6+repack-2_arm64.deb ... 82s Unpacking libhdf5-310:arm64 (1.14.6+repack-2) ... 82s Selecting previously unselected package libhdf5-hl-310:arm64. 82s Preparing to unpack .../08-libhdf5-hl-310_1.14.6+repack-2_arm64.deb ... 82s Unpacking libhdf5-hl-310:arm64 (1.14.6+repack-2) ... 82s Selecting previously unselected package libhtscodecs2:arm64. 82s Preparing to unpack .../09-libhtscodecs2_1.6.1-2build1_arm64.deb ... 82s Unpacking libhtscodecs2:arm64 (1.6.1-2build1) ... 82s Selecting previously unselected package libhts3t64:arm64. 83s Preparing to unpack .../10-libhts3t64_1.22.1+ds2-1_arm64.deb ... 83s Unpacking libhts3t64:arm64 (1.22.1+ds2-1) ... 83s Selecting previously unselected package liblzf1:arm64. 83s Preparing to unpack .../11-liblzf1_3.6-4build1_arm64.deb ... 83s Unpacking liblzf1:arm64 (3.6-4build1) ... 83s Selecting previously unselected package libqhull-r8.0:arm64. 83s Preparing to unpack .../12-libqhull-r8.0_2020.2-8_arm64.deb ... 83s Unpacking libqhull-r8.0:arm64 (2020.2-8) ... 83s Selecting previously unselected package python3-h5py-serial. 83s Preparing to unpack .../13-python3-h5py-serial_3.15.1-4_arm64.deb ... 83s Unpacking python3-h5py-serial (3.15.1-4) ... 83s Selecting previously unselected package python3-h5py. 83s Preparing to unpack .../14-python3-h5py_3.15.1-4_all.deb ... 83s Unpacking python3-h5py (3.15.1-4) ... 83s Selecting previously unselected package python3-pytz. 83s Preparing to unpack .../15-python3-pytz_2025.2-5_all.deb ... 83s Unpacking python3-pytz (2025.2-5) ... 83s Selecting previously unselected package python3-pandas-lib:arm64. 83s Preparing to unpack .../16-python3-pandas-lib_2.3.3+dfsg-3_arm64.deb ... 83s Unpacking python3-pandas-lib:arm64 (2.3.3+dfsg-3) ... 83s Selecting previously unselected package python3-pandas. 83s Preparing to unpack .../17-python3-pandas_2.3.3+dfsg-3_all.deb ... 83s Unpacking python3-pandas (2.3.3+dfsg-3) ... 83s Selecting previously unselected package python3-decorator. 83s Preparing to unpack .../18-python3-decorator_5.2.1-2_all.deb ... 83s Unpacking python3-decorator (5.2.1-2) ... 83s Selecting previously unselected package python3-fastjsonschema. 83s Preparing to unpack .../19-python3-fastjsonschema_2.21.1-1_all.deb ... 83s Unpacking python3-fastjsonschema (2.21.1-1) ... 83s Selecting previously unselected package python3-platformdirs. 83s Preparing to unpack .../20-python3-platformdirs_4.5.1-1_all.deb ... 83s Unpacking python3-platformdirs (4.5.1-1) ... 83s Selecting previously unselected package python3-traitlets. 83s Preparing to unpack .../21-python3-traitlets_5.14.3+really5.14.3-2_all.deb ... 83s Unpacking python3-traitlets (5.14.3+really5.14.3-2) ... 83s Selecting previously unselected package python3-jupyter-core. 83s Preparing to unpack .../22-python3-jupyter-core_5.9.1-1_all.deb ... 83s Unpacking python3-jupyter-core (5.9.1-1) ... 83s Selecting previously unselected package python3-nbformat. 83s Preparing to unpack .../23-python3-nbformat_5.10.4-1_all.deb ... 83s Unpacking python3-nbformat (5.10.4-1) ... 83s Selecting previously unselected package python3-tenacity. 83s Preparing to unpack .../24-python3-tenacity_9.0.0-0ubuntu1_all.deb ... 83s Unpacking python3-tenacity (9.0.0-0ubuntu1) ... 83s Selecting previously unselected package python3-plotly. 83s Preparing to unpack .../25-python3-plotly_5.20.0+dfsg-1.1_all.deb ... 83s Unpacking python3-plotly (5.20.0+dfsg-1.1) ... 84s Selecting previously unselected package python3-pysam. 84s Preparing to unpack .../26-python3-pysam_0.23.3+ds-2_arm64.deb ... 84s Unpacking python3-pysam (0.23.3+ds-2) ... 84s Selecting previously unselected package python3-scipy. 84s Preparing to unpack .../27-python3-scipy_1.16.3-4_arm64.deb ... 84s Unpacking python3-scipy (1.16.3-4) ... 85s Selecting previously unselected package python3-tqdm. 85s Preparing to unpack .../28-python3-tqdm_4.67.1-7_all.deb ... 85s Unpacking python3-tqdm (4.67.1-7) ... 85s Selecting previously unselected package pycoqc. 85s Preparing to unpack .../29-pycoqc_2.5.2+dfsg-4_all.deb ... 85s Unpacking pycoqc (2.5.2+dfsg-4) ... 85s Setting up libhtscodecs2:arm64 (1.6.1-2build1) ... 85s Setting up python3-tenacity (9.0.0-0ubuntu1) ... 85s Setting up python3-tqdm (4.67.1-7) ... 85s Setting up libdeflate0:arm64 (1.23-2) ... 85s Setting up libqhull-r8.0:arm64 (2020.2-8) ... 85s Setting up python3-pytz (2025.2-5) ... 85s Setting up python3-platformdirs (4.5.1-1) ... 86s Setting up python3-decorator (5.2.1-2) ... 86s Setting up libblas3:arm64 (3.12.1-7ubuntu1) ... 86s 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 86s Setting up liblzf1:arm64 (3.6-4build1) ... 86s Setting up python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 86s Setting up libgfortran5:arm64 (15.2.0-12ubuntu1) ... 86s Setting up python3-fastjsonschema (2.21.1-1) ... 86s Setting up python3-traitlets (5.14.3+really5.14.3-2) ... 86s Setting up libhts3t64:arm64 (1.22.1+ds2-1) ... 86s Setting up python3-jupyter-core (5.9.1-1) ... 86s Setting up libsz2:arm64 (1.1.5-1) ... 86s Setting up liblapack3:arm64 (3.12.1-7ubuntu1) ... 86s 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 86s Setting up python3-pysam (0.23.3+ds-2) ... 86s Setting up python3-nbformat (5.10.4-1) ... 86s Setting up python3-plotly (5.20.0+dfsg-1.1) ... 92s Setting up python3-numpy (1:2.3.5+ds-3) ... 93s Setting up libhdf5-310:arm64 (1.14.6+repack-2) ... 93s Setting up libhdf5-hl-310:arm64 (1.14.6+repack-2) ... 93s Setting up python3-scipy (1.16.3-4) ... 97s Setting up python3-pandas-lib:arm64 (2.3.3+dfsg-3) ... 97s Setting up python3-h5py-serial (3.15.1-4) ... 97s Setting up python3-pandas (2.3.3+dfsg-3) ... 101s Setting up python3-h5py (3.15.1-4) ... 101s Setting up pycoqc (2.5.2+dfsg-4) ... 101s Processing triggers for libc-bin (2.42-2ubuntu4) ... 101s Processing triggers for man-db (2.13.1-1) ... 103s autopkgtest [18:10:05]: test run-unit-test: [----------------------- 103s Test 1 104s Checking arguments values 104s Check input data files 104s Parse data files 104s Merge data 104s Cleaning data 104s Loading plotting interface 105s PASS 105s 105s Test 2 105s Checking arguments values 105s Check input data files 105s Parse data files 106s Merge data 106s Cleaning data 106s Loading plotting interface 106s PASS 106s 106s Test 3 107s Checking arguments values 107s Check input data files 107s Parse data files 107s Merge data 107s Cleaning data 107s Loading plotting interface 108s PASS 108s 108s Test 4 108s Checking arguments values 108s Check input data files 108s Parse data files 108s Merge data 108s Cleaning data 109s Loading plotting interface 109s PASS 109s 109s Test 5 110s Checking arguments values 110s Check input data files 110s Parse data files 110s Merge data 110s Cleaning data 110s Loading plotting interface 111s PASS 111s 111s Test 6 112s PASS 112s 112s Test 7 112s Checking arguments values 112s Check input data files 112s Parse data files 112s Merge data 112s Cleaning data 112s Loading plotting interface 113s PASS 113s 113s Test 8 114s 0 reads [00:00, ? reads/s] 22 reads [00:00, 1087.52 reads/s] 114s Total reads: 22 / Average speed: 545.25 reads/s 114s 114s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template 114s 37dfa1d5-5d84-486c-bf47-9eb6438f5645 40ebe55356ada6c830fa793745ef4c498d896c73 410 30 555 8.219 filtered_out 114s 9a1c5296-2ab1-4abd-8d50-e059754cf332 40ebe55356ada6c830fa793745ef4c498d896c73 319 33 1235 8.119 filtered_out 114s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out 114s ed05c5e6-7aab-4970-a431-3411047764a6 40ebe55356ada6c830fa793745ef4c498d896c73 224 34 880 8.891 filtered_out 114s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out 114s f8325de9-a77e-4616-a4a8-69ecf32e1688 40ebe55356ada6c830fa793745ef4c498d896c73 354 16 568 8.206 filtered_out 114s 4e21bf07-e2df-42d8-b347-59ef2c0618ea 40ebe55356ada6c830fa793745ef4c498d896c73 290 31 1160 8.741 filtered_out 114s 1f83ee80-ac29-46be-b8bc-9dc9325f1fa7 40ebe55356ada6c830fa793745ef4c498d896c73 382 35 819 7.414 filtered_out 114s 6af04302-04c8-4d8d-8e87-aa69178b3f24 40ebe55356ada6c830fa793745ef4c498d896c73 36 26 832 8.234 filtered_out 114s PASS 114s 114s Test 9 115s Check input data and options 115s Start processing fast5 files 115s 0 reads [00:00, ? reads/s] 22 reads [00:00, 2577.29 reads/s] 115s Overall counts valid files: 22 115s 115s fields found mean_qscore_template: 22 115s called_events: 22 115s duration: 22 115s strand_score: 22 115s 115s fields not found 115s Total reads: 22 / Average speed: 794.52 reads/s 115s 115s mean_qscore_template called_events duration strand_score 115s 7.805 1438 21583 -0.0006 115s 8.219 2080 31208 -0.0011 115s 8.119 3181 47720 -0.0004 115s 8.891 2774 41612 -0.0006 115s 8.56 5838 87570 -0.0003 115s 8.741 3117 46767 -0.0006 115s 7.414 3017 45267 -0.0002 115s 8.234 1827 27409 -0.0011 115s 8.206 1649 24747 -0.0009 115s PASS 115s 115s Test 10 115s Check input data and options 115s Start processing fast5 files 115s 0 reads [00:00, ? reads/s] 22 reads [00:00, 899.84 reads/s] 115s Overall counts valid files: 22 115s 115s fields found read_id: 22 115s run_id: 22 115s channel: 22 115s start_time: 22 115s sequence_length_template: 22 115s mean_qscore_template: 22 115s calibration_strand_genome_template: 22 115s 115s fields not found barcode_arrangement: 22 115s 115s Total reads: 22 / Average speed: 561.31 reads/s 115s 116s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template path 116s 37dfa1d5-5d84-486c-bf47-9eb6438f5645 40ebe55356ada6c830fa793745ef4c498d896c73 410 30 555 8.219 filtered_out /tmp/autopkgtest.dS36J0/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_410_strand.fast5 116s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out /tmp/autopkgtest.dS36J0/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_121_strand.fast5 116s 9a1c5296-2ab1-4abd-8d50-e059754cf332 40ebe55356ada6c830fa793745ef4c498d896c73 319 33 1235 8.119 filtered_out /tmp/autopkgtest.dS36J0/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_319_strand.fast5 116s ed05c5e6-7aab-4970-a431-3411047764a6 40ebe55356ada6c830fa793745ef4c498d896c73 224 34 880 8.891 filtered_out /tmp/autopkgtest.dS36J0/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_224_strand.fast5 116s f8325de9-a77e-4616-a4a8-69ecf32e1688 40ebe55356ada6c830fa793745ef4c498d896c73 354 16 568 8.206 filtered_out /tmp/autopkgtest.dS36J0/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_354_strand.fast5 116s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out /tmp/autopkgtest.dS36J0/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_103_strand.fast5 116s 4e21bf07-e2df-42d8-b347-59ef2c0618ea 40ebe55356ada6c830fa793745ef4c498d896c73 290 31 1160 8.741 filtered_out /tmp/autopkgtest.dS36J0/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_290_strand.fast5 116s 1f83ee80-ac29-46be-b8bc-9dc9325f1fa7 40ebe55356ada6c830fa793745ef4c498d896c73 382 35 819 7.414 filtered_out /tmp/autopkgtest.dS36J0/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_382_strand.fast5 116s 6af04302-04c8-4d8d-8e87-aa69178b3f24 40ebe55356ada6c830fa793745ef4c498d896c73 36 26 832 8.234 filtered_out /tmp/autopkgtest.dS36J0/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_36_strand.fast5 116s PASS 116s 116s Test 11 116s Import data from sequencing summary file(s) and cleanup 116s Read files and import in a dataframe 116s Check input data files 116s Parse data files 117s Merge data 117s Cleanup missing barcodes values 117s Cleaning up low frequency barcodes 117s Split data per barcode 117s Processing data for Barcode barcode02 117s Processing data for Barcode barcode07 117s Processing data for Barcode barcode08 117s Processing data for Barcode barcode09 117s Processing data for Barcode barcode10 117s Processing data for Barcode barcode11 117s Processing data for Barcode barcode12 118s Processing data for Barcode unclassified 118s Barcode Counts 118s Counts Write 118s barcode02 2 False 118s barcode07 1 False 118s barcode08 30 False 118s barcode09 9945 True 118s barcode10 12644 True 118s barcode11 13594 True 118s barcode12 9813 True 118s unclassified 3971 False 118s PASS 118s 118s Test 12 118s General info 118s package_name: pycoQC 118s package_version: 2.5.2 118s timestamp: 2026-02-03 18:10:20.858114 118s 118s Runtime options 118s summary_file: ['Guppy-basecall-1D-DNA_sequencing_summary.txt'] 118s barcode_file: ['Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt'] 118s output_dir: results/ 118s output_unclassified: False 118s min_barcode_percent: 0.1 118s verbose: True 118s quiet: False 118s 118s Import data from sequencing summary file(s) and cleanup 118s Read files and import in a dataframe 118s Check input data files 118s Sequencing summary files found: Guppy-basecall-1D-DNA_sequencing_summary.txt 118s Barcode files found: Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt 118s Parse data files 118s Parse summary files 119s 3,999 reads found in initial file 119s Parse barcode files 119s Found valid Deepbinner barcode file 119s 3,775 reads with barcodes assigned 119s Merge data 119s Cleanup missing barcodes values 119s Cleaning up low frequency barcodes 119s Split data per barcode 119s Processing data for Barcode 1 119s Processing data for Barcode 2 119s Processing data for Barcode 3 119s Processing data for Barcode 4 119s Processing data for Barcode 5 119s Processing data for Barcode 6 119s Processing data for Barcode 7 119s Processing data for Barcode 8 119s Processing data for Barcode unclassified 119s Barcode Counts 119s Counts Write 119s 1 534 True 119s 2 206 True 119s 3 562 True 119s 4 579 True 119s 5 590 True 119s 6 655 True 119s 7 271 True 119s 8 378 True 119s unclassified 224 False 119s PASS 119s 119s Check if files really exist 119s PASS 119s 119s autopkgtest [18:10:21]: test run-unit-test: -----------------------] 120s run-unit-test PASS 120s autopkgtest [18:10:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 120s autopkgtest [18:10:22]: @@@@@@@@@@@@@@@@@@@@ summary 120s run-unit-test PASS