0s autopkgtest [18:52:02]: starting date and time: 2026-02-03 18:52:02+0000 0s autopkgtest [18:52:02]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [18:52:02]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.cjekvgnv/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-ppc64el-20.secgroup --name adt-resolute-ppc64el-pycoqc-20260203-185202-juju-7f2275-prod-proposed-migration-environment-15-08d56ffc-9d59-4196-90ef-8d3d7aac3890 --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-ppc64el-pycoqc-20260203-185202-juju-7f2275-prod-proposed-migration-environment-15-08d56ffc-9d59-4196-90ef-8d3d7aac3890 from image adt/ubuntu-resolute-ppc64el-server-20260202.img (UUID ca98045c-2f99-4634-a243-9d47350236de)... 50s autopkgtest [18:52:52]: testbed dpkg architecture: ppc64el 50s autopkgtest [18:52:52]: testbed apt version: 3.1.14 51s autopkgtest [18:52:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 51s autopkgtest [18:52:53]: testbed release detected to be: None 51s autopkgtest [18:52:53]: updating testbed package index (apt update) 52s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 52s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 52s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 52s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 52s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [27.9 kB] 52s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 52s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1327 kB] 52s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [241 kB] 52s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [286 kB] 52s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [1148 kB] 52s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [17.8 kB] 53s Fetched 3178 kB in 1s (3564 kB/s) 53s Reading package lists... 54s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 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 55s Reading package lists... 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s Calculating upgrade... 56s The following packages will be upgraded: 56s cloud-init cloud-init-base firmware-sof-signed libexpat1 56s liblocale-gettext-perl powermgmt-base powerpc-ibm-utils powerpc-utils 56s ppc64-diag python3-jinja2 systemd-hwe-hwdb 56s 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s Need to get 3139 kB of archives. 56s After this operation, 3072 B of additional disk space will be used. 56s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el libexpat1 ppc64el 2.7.4-1 [106 kB] 56s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblocale-gettext-perl ppc64el 1.07-8 [16.3 kB] 56s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el powerpc-ibm-utils ppc64el 1.3.13-2build1 [263 kB] 56s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el ppc64-diag ppc64el 2.7.9-1.1ubuntu2 [310 kB] 56s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el firmware-sof-signed all 2025.05.1-1build1 [1696 kB] 56s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el powerpc-utils ppc64el 1.3.13-2build1 [1638 B] 56s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el systemd-hwe-hwdb all 259.0.1 [3152 B] 56s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el powermgmt-base all 1.38ubuntu2 [7878 B] 56s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el cloud-init-base all 25.4~4g26c7d38d-0ubuntu1 [624 kB] 56s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el cloud-init all 25.4~4g26c7d38d-0ubuntu1 [2120 B] 56s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-jinja2 all 3.1.6-1build1 [109 kB] 56s dpkg-preconfigure: unable to re-open stdin: No such file or directory 56s Fetched 3139 kB in 1s (6097 kB/s) 57s (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 ... 82007 files and directories currently installed.) 57s Preparing to unpack .../00-libexpat1_2.7.4-1_ppc64el.deb ... 57s Unpacking libexpat1:ppc64el (2.7.4-1) over (2.7.3-1) ... 57s Preparing to unpack .../01-liblocale-gettext-perl_1.07-8_ppc64el.deb ... 57s Unpacking liblocale-gettext-perl (1.07-8) over (1.07-7build1) ... 57s Preparing to unpack .../02-powerpc-ibm-utils_1.3.13-2build1_ppc64el.deb ... 57s Unpacking powerpc-ibm-utils (1.3.13-2build1) over (1.3.13-2) ... 58s Preparing to unpack .../03-ppc64-diag_2.7.9-1.1ubuntu2_ppc64el.deb ... 58s Unpacking ppc64-diag (2.7.9-1.1ubuntu2) over (2.7.9-1.1ubuntu1) ... 58s Preparing to unpack .../04-firmware-sof-signed_2025.05.1-1build1_all.deb ... 58s Unpacking firmware-sof-signed (2025.05.1-1build1) over (2025.05.1-1) ... 58s Preparing to unpack .../05-powerpc-utils_1.3.13-2build1_ppc64el.deb ... 58s Unpacking powerpc-utils (1.3.13-2build1) over (1.3.13-2) ... 58s Preparing to unpack .../06-systemd-hwe-hwdb_259.0.1_all.deb ... 58s Unpacking systemd-hwe-hwdb (259.0.1) over (257.7.1) ... 58s Preparing to unpack .../07-powermgmt-base_1.38ubuntu2_all.deb ... 58s Unpacking powermgmt-base (1.38ubuntu2) over (1.38ubuntu1) ... 58s Preparing to unpack .../08-cloud-init-base_25.4~4g26c7d38d-0ubuntu1_all.deb ... 58s Unpacking cloud-init-base (25.4~4g26c7d38d-0ubuntu1) over (25.4~3g78f6f15e-0ubuntu1) ... 59s Preparing to unpack .../09-cloud-init_25.4~4g26c7d38d-0ubuntu1_all.deb ... 59s Unpacking cloud-init (25.4~4g26c7d38d-0ubuntu1) over (25.4~3g78f6f15e-0ubuntu1) ... 59s Preparing to unpack .../10-python3-jinja2_3.1.6-1build1_all.deb ... 59s Unpacking python3-jinja2 (3.1.6-1build1) over (3.1.6-1) ... 59s Setting up libexpat1:ppc64el (2.7.4-1) ... 59s Setting up powermgmt-base (1.38ubuntu2) ... 59s Setting up firmware-sof-signed (2025.05.1-1build1) ... 59s Setting up powerpc-ibm-utils (1.3.13-2build1) ... 59s Setting up powerpc-utils (1.3.13-2build1) ... 59s Setting up python3-jinja2 (3.1.6-1build1) ... 60s Setting up systemd-hwe-hwdb (259.0.1) ... 60s Setting up ppc64-diag (2.7.9-1.1ubuntu2) ... 62s Setting up liblocale-gettext-perl (1.07-8) ... 62s Setting up cloud-init-base (25.4~4g26c7d38d-0ubuntu1) ... 62s Clearing ignored debconf value cloud-init/datasources 62s Encountered debconf setting for cloud-init-base/datasources. 63s Setting up cloud-init (25.4~4g26c7d38d-0ubuntu1) ... 63s Processing triggers for rsyslog (8.2512.0-1ubuntu2) ... 64s Processing triggers for man-db (2.13.1-1) ... 65s Processing triggers for udev (259-1ubuntu3) ... 66s Processing triggers for libc-bin (2.42-2ubuntu4) ... 66s autopkgtest [18:53:08]: upgrading testbed (apt dist-upgrade and autopurge) 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s Calculating upgrade... 67s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Solving dependencies... 67s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s autopkgtest [18:53:09]: rebooting testbed after setup commands that affected boot 105s autopkgtest [18:53:47]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:45:54 UTC 2026 107s autopkgtest [18:53:49]: @@@@@@@@@@@@@@@@@@@@ apt-source pycoqc 110s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (dsc) [2027 B] 110s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (tar) [41.6 MB] 110s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (diff) [6840 B] 110s gpgv: Signature made Sat Jan 18 02:09:23 2025 UTC 110s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 110s gpgv: issuer "tchet@debian.org" 110s gpgv: Can't check signature: No public key 110s dpkg-source: warning: cannot verify inline signature for ./pycoqc_2.5.2+dfsg-4.dsc: no acceptable signature found 112s autopkgtest [18:53:54]: testing package pycoqc version 2.5.2+dfsg-4 113s autopkgtest [18:53:55]: build not needed 117s autopkgtest [18:53:59]: test run-unit-test: preparing testbed 117s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Solving dependencies... 118s The following NEW packages will be installed: 118s libblas3 libdeflate0 libgfortran5 libhdf5-310 libhdf5-hl-310 libhts3t64 118s libhtscodecs2 liblapack3 liblzf1 libqhull-r8.0 libsz2 pycoqc 118s python3-decorator python3-fastjsonschema python3-h5py python3-h5py-serial 118s python3-jupyter-core python3-nbformat python3-numpy python3-numpy-dev 118s python3-pandas python3-pandas-lib python3-platformdirs python3-plotly 118s python3-pysam python3-pytz python3-scipy python3-tenacity python3-tqdm 118s python3-traitlets 118s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 118s Need to get 53.2 MB of archives. 118s After this operation, 377 MB of additional disk space will be used. 118s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy-dev ppc64el 1:2.3.5+ds-3 [153 kB] 118s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-7ubuntu1 [291 kB] 118s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-12ubuntu1 [620 kB] 118s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-7ubuntu1 [2960 kB] 118s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy ppc64el 1:2.3.5+ds-3 [5722 kB] 118s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2 [63.3 kB] 118s Get:7 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libsz2 ppc64el 1.1.5-1 [25.3 kB] 118s Get:8 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhdf5-310 ppc64el 1.14.6+repack-2 [1545 kB] 118s Get:9 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhdf5-hl-310 ppc64el 1.14.6+repack-2 [76.3 kB] 118s Get:10 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhtscodecs2 ppc64el 1.6.1-2build1 [119 kB] 118s Get:11 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhts3t64 ppc64el 1.22.1+ds2-1 [617 kB] 118s Get:12 http://ftpmaster.internal/ubuntu resolute/universe ppc64el liblzf1 ppc64el 3.6-4build1 [8064 B] 118s Get:13 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libqhull-r8.0 ppc64el 2020.2-8 [227 kB] 118s Get:14 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-h5py-serial ppc64el 3.15.1-4 [1668 kB] 118s Get:15 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-h5py all 3.15.1-4 [11.3 kB] 118s Get:16 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pytz all 2025.2-5 [32.4 kB] 119s Get:17 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pandas-lib ppc64el 2.3.3+dfsg-3 [7213 kB] 119s Get:18 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pandas all 2.3.3+dfsg-3 [2948 kB] 119s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-decorator all 5.2.1-2 [28.1 kB] 119s Get:20 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-fastjsonschema all 2.21.1-1 [20.4 kB] 119s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-platformdirs all 4.5.1-1 [17.1 kB] 119s Get:22 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-traitlets all 5.14.3+really5.14.3-2 [71.7 kB] 119s Get:23 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-jupyter-core all 5.9.1-1 [28.9 kB] 119s Get:24 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-nbformat all 5.10.4-1 [39.2 kB] 119s Get:25 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-tenacity all 9.0.0-0ubuntu1 [17.0 kB] 119s Get:26 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-plotly all 5.20.0+dfsg-1.1 [2766 kB] 119s Get:27 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pysam ppc64el 0.23.3+ds-2 [5011 kB] 119s Get:28 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-scipy ppc64el 1.16.3-4 [20.7 MB] 120s Get:29 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-tqdm all 4.67.1-7 [93.3 kB] 120s Get:30 http://ftpmaster.internal/ubuntu resolute/universe ppc64el pycoqc all 2.5.2+dfsg-4 [36.4 kB] 120s Fetched 53.2 MB in 2s (27.1 MB/s) 120s Selecting previously unselected package python3-numpy-dev:ppc64el. 121s (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 ... 82008 files and directories currently installed.) 121s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_ppc64el.deb ... 121s Unpacking python3-numpy-dev:ppc64el (1:2.3.5+ds-3) ... 121s Selecting previously unselected package libblas3:ppc64el. 121s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_ppc64el.deb ... 121s Unpacking libblas3:ppc64el (3.12.1-7ubuntu1) ... 121s Selecting previously unselected package libgfortran5:ppc64el. 121s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_ppc64el.deb ... 121s Unpacking libgfortran5:ppc64el (15.2.0-12ubuntu1) ... 121s Selecting previously unselected package liblapack3:ppc64el. 121s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_ppc64el.deb ... 121s Unpacking liblapack3:ppc64el (3.12.1-7ubuntu1) ... 121s Selecting previously unselected package python3-numpy. 121s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_ppc64el.deb ... 121s Unpacking python3-numpy (1:2.3.5+ds-3) ... 121s Selecting previously unselected package libdeflate0:ppc64el. 121s Preparing to unpack .../05-libdeflate0_1.23-2_ppc64el.deb ... 121s Unpacking libdeflate0:ppc64el (1.23-2) ... 121s Selecting previously unselected package libsz2:ppc64el. 121s Preparing to unpack .../06-libsz2_1.1.5-1_ppc64el.deb ... 121s Unpacking libsz2:ppc64el (1.1.5-1) ... 121s Selecting previously unselected package libhdf5-310:ppc64el. 121s Preparing to unpack .../07-libhdf5-310_1.14.6+repack-2_ppc64el.deb ... 121s Unpacking libhdf5-310:ppc64el (1.14.6+repack-2) ... 121s Selecting previously unselected package libhdf5-hl-310:ppc64el. 121s Preparing to unpack .../08-libhdf5-hl-310_1.14.6+repack-2_ppc64el.deb ... 121s Unpacking libhdf5-hl-310:ppc64el (1.14.6+repack-2) ... 121s Selecting previously unselected package libhtscodecs2:ppc64el. 121s Preparing to unpack .../09-libhtscodecs2_1.6.1-2build1_ppc64el.deb ... 121s Unpacking libhtscodecs2:ppc64el (1.6.1-2build1) ... 121s Selecting previously unselected package libhts3t64:ppc64el. 121s Preparing to unpack .../10-libhts3t64_1.22.1+ds2-1_ppc64el.deb ... 121s Unpacking libhts3t64:ppc64el (1.22.1+ds2-1) ... 121s Selecting previously unselected package liblzf1:ppc64el. 121s Preparing to unpack .../11-liblzf1_3.6-4build1_ppc64el.deb ... 121s Unpacking liblzf1:ppc64el (3.6-4build1) ... 121s Selecting previously unselected package libqhull-r8.0:ppc64el. 121s Preparing to unpack .../12-libqhull-r8.0_2020.2-8_ppc64el.deb ... 121s Unpacking libqhull-r8.0:ppc64el (2020.2-8) ... 121s Selecting previously unselected package python3-h5py-serial. 121s Preparing to unpack .../13-python3-h5py-serial_3.15.1-4_ppc64el.deb ... 121s Unpacking python3-h5py-serial (3.15.1-4) ... 121s Selecting previously unselected package python3-h5py. 121s Preparing to unpack .../14-python3-h5py_3.15.1-4_all.deb ... 121s Unpacking python3-h5py (3.15.1-4) ... 121s Selecting previously unselected package python3-pytz. 121s Preparing to unpack .../15-python3-pytz_2025.2-5_all.deb ... 121s Unpacking python3-pytz (2025.2-5) ... 121s Selecting previously unselected package python3-pandas-lib:ppc64el. 121s Preparing to unpack .../16-python3-pandas-lib_2.3.3+dfsg-3_ppc64el.deb ... 121s Unpacking python3-pandas-lib:ppc64el (2.3.3+dfsg-3) ... 122s Selecting previously unselected package python3-pandas. 122s Preparing to unpack .../17-python3-pandas_2.3.3+dfsg-3_all.deb ... 122s Unpacking python3-pandas (2.3.3+dfsg-3) ... 122s Selecting previously unselected package python3-decorator. 122s Preparing to unpack .../18-python3-decorator_5.2.1-2_all.deb ... 122s Unpacking python3-decorator (5.2.1-2) ... 122s Selecting previously unselected package python3-fastjsonschema. 122s Preparing to unpack .../19-python3-fastjsonschema_2.21.1-1_all.deb ... 122s Unpacking python3-fastjsonschema (2.21.1-1) ... 122s Selecting previously unselected package python3-platformdirs. 122s Preparing to unpack .../20-python3-platformdirs_4.5.1-1_all.deb ... 122s Unpacking python3-platformdirs (4.5.1-1) ... 122s Selecting previously unselected package python3-traitlets. 122s Preparing to unpack .../21-python3-traitlets_5.14.3+really5.14.3-2_all.deb ... 122s Unpacking python3-traitlets (5.14.3+really5.14.3-2) ... 122s Selecting previously unselected package python3-jupyter-core. 122s Preparing to unpack .../22-python3-jupyter-core_5.9.1-1_all.deb ... 122s Unpacking python3-jupyter-core (5.9.1-1) ... 122s Selecting previously unselected package python3-nbformat. 122s Preparing to unpack .../23-python3-nbformat_5.10.4-1_all.deb ... 122s Unpacking python3-nbformat (5.10.4-1) ... 122s Selecting previously unselected package python3-tenacity. 122s Preparing to unpack .../24-python3-tenacity_9.0.0-0ubuntu1_all.deb ... 122s Unpacking python3-tenacity (9.0.0-0ubuntu1) ... 122s Selecting previously unselected package python3-plotly. 122s Preparing to unpack .../25-python3-plotly_5.20.0+dfsg-1.1_all.deb ... 122s Unpacking python3-plotly (5.20.0+dfsg-1.1) ... 124s Selecting previously unselected package python3-pysam. 124s Preparing to unpack .../26-python3-pysam_0.23.3+ds-2_ppc64el.deb ... 124s Unpacking python3-pysam (0.23.3+ds-2) ... 124s Selecting previously unselected package python3-scipy. 124s Preparing to unpack .../27-python3-scipy_1.16.3-4_ppc64el.deb ... 124s Unpacking python3-scipy (1.16.3-4) ... 124s Selecting previously unselected package python3-tqdm. 124s Preparing to unpack .../28-python3-tqdm_4.67.1-7_all.deb ... 124s Unpacking python3-tqdm (4.67.1-7) ... 125s Selecting previously unselected package pycoqc. 125s Preparing to unpack .../29-pycoqc_2.5.2+dfsg-4_all.deb ... 125s Unpacking pycoqc (2.5.2+dfsg-4) ... 125s Setting up libhtscodecs2:ppc64el (1.6.1-2build1) ... 125s Setting up python3-tenacity (9.0.0-0ubuntu1) ... 125s Setting up python3-tqdm (4.67.1-7) ... 125s Setting up libdeflate0:ppc64el (1.23-2) ... 125s Setting up libqhull-r8.0:ppc64el (2020.2-8) ... 125s Setting up python3-pytz (2025.2-5) ... 125s Setting up python3-platformdirs (4.5.1-1) ... 125s Setting up python3-decorator (5.2.1-2) ... 125s Setting up libblas3:ppc64el (3.12.1-7ubuntu1) ... 125s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 125s Setting up liblzf1:ppc64el (3.6-4build1) ... 125s Setting up python3-numpy-dev:ppc64el (1:2.3.5+ds-3) ... 125s Setting up libgfortran5:ppc64el (15.2.0-12ubuntu1) ... 125s Setting up python3-fastjsonschema (2.21.1-1) ... 125s Setting up python3-traitlets (5.14.3+really5.14.3-2) ... 125s Setting up libhts3t64:ppc64el (1.22.1+ds2-1) ... 125s Setting up python3-jupyter-core (5.9.1-1) ... 125s Setting up libsz2:ppc64el (1.1.5-1) ... 125s Setting up liblapack3:ppc64el (3.12.1-7ubuntu1) ... 125s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 125s Setting up python3-pysam (0.23.3+ds-2) ... 126s Setting up python3-nbformat (5.10.4-1) ... 126s Setting up python3-plotly (5.20.0+dfsg-1.1) ... 132s Setting up python3-numpy (1:2.3.5+ds-3) ... 134s Setting up libhdf5-310:ppc64el (1.14.6+repack-2) ... 134s Setting up libhdf5-hl-310:ppc64el (1.14.6+repack-2) ... 134s Setting up python3-scipy (1.16.3-4) ... 138s Setting up python3-pandas-lib:ppc64el (2.3.3+dfsg-3) ... 138s Setting up python3-h5py-serial (3.15.1-4) ... 138s Setting up python3-pandas (2.3.3+dfsg-3) ... 143s Setting up python3-h5py (3.15.1-4) ... 143s Setting up pycoqc (2.5.2+dfsg-4) ... 143s Processing triggers for libc-bin (2.42-2ubuntu4) ... 143s Processing triggers for man-db (2.13.1-1) ... 147s autopkgtest [18:54:29]: test run-unit-test: [----------------------- 147s Test 1 149s Checking arguments values 149s Check input data files 149s Parse data files 149s Merge data 149s Cleaning data 149s Loading plotting interface 149s PASS 149s 149s Test 2 150s Checking arguments values 150s Check input data files 150s Parse data files 150s Merge data 150s Cleaning data 150s Loading plotting interface 151s PASS 151s 151s Test 3 151s Checking arguments values 151s Check input data files 151s Parse data files 151s Merge data 151s Cleaning data 151s Loading plotting interface 152s PASS 152s 152s Test 4 153s Checking arguments values 153s Check input data files 153s Parse data files 153s Merge data 153s Cleaning data 153s Loading plotting interface 154s PASS 154s 154s Test 5 154s Checking arguments values 154s Check input data files 154s Parse data files 154s Merge data 154s Cleaning data 154s Loading plotting interface 155s PASS 155s 155s Test 6 156s PASS 156s 156s Test 7 156s Checking arguments values 156s Check input data files 156s Parse data files 156s Merge data 156s Cleaning data 156s Loading plotting interface 157s PASS 157s 157s Test 8 158s 0 reads [00:00, ? reads/s] 22 reads [00:00, 1462.61 reads/s] 158s Total reads: 22 / Average speed: 580.02 reads/s 158s 158s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template 158s 5b7fadd0-c646-4c7b-9800-66ee658a5ca8 40ebe55356ada6c830fa793745ef4c498d896c73 150 37 468 7.608 filtered_out 158s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out 158s c38cbad9-d91e-4208-9317-832f4e2cc289 40ebe55356ada6c830fa793745ef4c498d896c73 113 30 824 8.693 filtered_out 158s 1f83ee80-ac29-46be-b8bc-9dc9325f1fa7 40ebe55356ada6c830fa793745ef4c498d896c73 382 35 819 7.414 filtered_out 158s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out 158s 4e21bf07-e2df-42d8-b347-59ef2c0618ea 40ebe55356ada6c830fa793745ef4c498d896c73 290 31 1160 8.741 filtered_out 158s f8325de9-a77e-4616-a4a8-69ecf32e1688 40ebe55356ada6c830fa793745ef4c498d896c73 354 16 568 8.206 filtered_out 158s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out 158s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out 158s PASS 158s 158s Test 9 158s Check input data and options 158s Start processing fast5 files 158s 0 reads [00:00, ? reads/s] 22 reads [00:00, 1024.28 reads/s] 158s Overall counts valid files: 22 158s 158s fields found mean_qscore_template: 22 158s called_events: 22 158s duration: 22 158s strand_score: 22 158s 158s fields not found 158s Total reads: 22 / Average speed: 683.16 reads/s 158s 159s mean_qscore_template called_events duration strand_score 159s 8.56 5838 87570 -0.0003 159s 8.693 2383 35752 -0.0005 159s 7.608 1615 24233 -0.0007 159s 7.414 3017 45267 -0.0002 159s 8.206 1649 24747 -0.0009 159s 8.741 3117 46767 -0.0006 159s 8.304 1547 23218 -0.0008 159s 9.407 2848 42730 -0.0003 159s 8.54 2023 30405 -0.0003 159s PASS 159s 159s Test 10 159s Check input data and options 159s Start processing fast5 files 159s 0 reads [00:00, ? reads/s] 22 reads [00:00, 671.69 reads/s] 159s Overall counts valid files: 22 159s 159s fields found read_id: 22 159s run_id: 22 159s channel: 22 159s start_time: 22 159s sequence_length_template: 22 159s mean_qscore_template: 22 159s calibration_strand_genome_template: 22 159s 159s fields not found barcode_arrangement: 22 159s 159s Total reads: 22 / Average speed: 511.25 reads/s 159s 159s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template path 159s 5b7fadd0-c646-4c7b-9800-66ee658a5ca8 40ebe55356ada6c830fa793745ef4c498d896c73 150 37 468 7.608 filtered_out /tmp/autopkgtest.c2AOfk/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_150_strand.fast5 159s c38cbad9-d91e-4208-9317-832f4e2cc289 40ebe55356ada6c830fa793745ef4c498d896c73 113 30 824 8.693 filtered_out /tmp/autopkgtest.c2AOfk/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_113_strand.fast5 159s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out /tmp/autopkgtest.c2AOfk/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_103_strand.fast5 159s 1f83ee80-ac29-46be-b8bc-9dc9325f1fa7 40ebe55356ada6c830fa793745ef4c498d896c73 382 35 819 7.414 filtered_out /tmp/autopkgtest.c2AOfk/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_382_strand.fast5 159s 4e21bf07-e2df-42d8-b347-59ef2c0618ea 40ebe55356ada6c830fa793745ef4c498d896c73 290 31 1160 8.741 filtered_out /tmp/autopkgtest.c2AOfk/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_290_strand.fast5 159s f8325de9-a77e-4616-a4a8-69ecf32e1688 40ebe55356ada6c830fa793745ef4c498d896c73 354 16 568 8.206 filtered_out /tmp/autopkgtest.c2AOfk/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_354_strand.fast5 159s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out /tmp/autopkgtest.c2AOfk/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_318_strand.fast5 159s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out /tmp/autopkgtest.c2AOfk/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_121_strand.fast5 159s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out /tmp/autopkgtest.c2AOfk/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_108_strand.fast5 159s PASS 159s 159s Test 11 160s Import data from sequencing summary file(s) and cleanup 160s Read files and import in a dataframe 160s Check input data files 160s Parse data files 160s Merge data 160s Cleanup missing barcodes values 160s Cleaning up low frequency barcodes 160s Split data per barcode 160s Processing data for Barcode barcode02 160s Processing data for Barcode barcode07 160s Processing data for Barcode barcode08 160s Processing data for Barcode barcode09 160s Processing data for Barcode barcode10 161s Processing data for Barcode barcode11 161s Processing data for Barcode barcode12 161s Processing data for Barcode unclassified 161s Barcode Counts 161s Counts Write 161s barcode02 2 False 161s barcode07 1 False 161s barcode08 30 False 161s barcode09 9945 True 161s barcode10 12644 True 161s barcode11 13594 True 161s barcode12 9813 True 161s unclassified 3971 False 161s PASS 161s 161s Test 12 162s General info 162s package_name: pycoQC 162s package_version: 2.5.2 162s timestamp: 2026-02-03 18:54:43.075995 162s 162s Runtime options 162s summary_file: ['Guppy-basecall-1D-DNA_sequencing_summary.txt'] 162s barcode_file: ['Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt'] 162s output_dir: results/ 162s output_unclassified: False 162s min_barcode_percent: 0.1 162s verbose: True 162s quiet: False 162s 162s Import data from sequencing summary file(s) and cleanup 162s Read files and import in a dataframe 162s Check input data files 162s Sequencing summary files found: Guppy-basecall-1D-DNA_sequencing_summary.txt 162s Barcode files found: Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt 162s Parse data files 162s Parse summary files 162s 3,999 reads found in initial file 162s Parse barcode files 162s Found valid Deepbinner barcode file 162s 3,775 reads with barcodes assigned 162s Merge data 162s Cleanup missing barcodes values 162s Cleaning up low frequency barcodes 162s Split data per barcode 162s Processing data for Barcode 1 162s Processing data for Barcode 2 162s Processing data for Barcode 3 162s Processing data for Barcode 4 162s Processing data for Barcode 5 162s Processing data for Barcode 6 162s Processing data for Barcode 7 162s Processing data for Barcode 8 162s Processing data for Barcode unclassified 162s Barcode Counts 162s Counts Write 162s 1 534 True 162s 2 206 True 162s 3 562 True 162s 4 579 True 162s 5 590 True 162s 6 655 True 162s 7 271 True 162s 8 378 True 162s unclassified 224 False 162s PASS 162s 162s Check if files really exist 162s PASS 162s 162s autopkgtest [18:54:44]: test run-unit-test: -----------------------] 163s run-unit-test PASS 163s autopkgtest [18:54:45]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 163s autopkgtest [18:54:45]: @@@@@@@@@@@@@@@@@@@@ summary 163s run-unit-test PASS