0s autopkgtest [10:24:37]: starting date and time: 2026-02-06 10:24:37+0000 0s autopkgtest [10:24:37]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [10:24:37]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.exy4u6f3/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-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-37.secgroup --name adt-resolute-amd64-pycoqc-20260206-102437-juju-7f2275-prod-proposed-migration-environment-2-9154393b-ab3c-42ad-b32c-4ab752e4024b --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-pycoqc-20260206-102437-juju-7f2275-prod-proposed-migration-environment-2-9154393b-ab3c-42ad-b32c-4ab752e4024b from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)... 75s autopkgtest [10:25:52]: testbed dpkg architecture: amd64 75s autopkgtest [10:25:52]: testbed apt version: 3.1.14 76s autopkgtest [10:25:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 76s autopkgtest [10:25:53]: testbed release detected to be: None 76s autopkgtest [10:25:53]: updating testbed package index (apt update) 76s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 77s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 77s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 77s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 77s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [30.8 kB] 77s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [6396 B] 77s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [192 kB] 77s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1491 kB] 77s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [247 kB] 77s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [185 kB] 77s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [7520 B] 77s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [44.8 kB] 77s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3692 B] 77s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 77s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [519 kB] 77s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1356 kB] 77s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [37.6 kB] 77s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4320 B] 78s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [26.7 kB] 78s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [1060 B] 78s Fetched 4277 kB in 1s (3790 kB/s) 79s Reading package lists... 80s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 80s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 80s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 80s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 80s Reading package lists... 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 81s Calculating upgrade... 81s The following packages will be upgraded: 81s amd64-microcode busybox-initramfs busybox-static dmsetup findutils less 81s libattr1 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common libdrm2 libgpm2 81s libkeyutils1 libmaxminddb0 libnpth0t64 libsensors-config libsensors5 mawk 81s patch pollinate python3-jinja2 python3-linkify-it python3-markdown-it 81s python3-referencing sed tar 81s 26 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s Need to get 3461 kB of archives. 81s After this operation, 270 kB disk space will be freed. 81s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB] 81s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB] 81s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB] 81s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB] 81s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB] 81s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB] 81s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB] 81s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB] 81s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB] 81s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 81s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB] 81s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB] 81s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B] 81s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB] 81s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB] 81s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB] 81s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B] 81s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB] 81s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB] 81s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB] 81s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B] 81s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB] 81s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB] 81s Get:24 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-jinja2 all 3.1.6-1build1 [109 kB] 81s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 81s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB] 81s dpkg-preconfigure: unable to re-open stdin: No such file or directory 81s Fetched 3461 kB in 0s (9179 kB/s) 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 ... 83957 files and directories currently installed.) 82s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ... 82s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ... 82s Setting up findutils (4.10.0-3build2) ... 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 ... 83957 files and directories currently installed.) 82s Preparing to unpack .../sed_4.9-2build3_amd64.deb ... 82s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 82s Setting up sed (4.9-2build3) ... 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 ... 83957 files and directories currently installed.) 82s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ... 82s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ... 82s Setting up tar (1.35+dfsg-3.1build2) ... 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 ... 83957 files and directories currently installed.) 82s Preparing to unpack .../libattr1_1%3a2.5.2-3build2_amd64.deb ... 82s Unpacking libattr1:amd64 (1:2.5.2-3build2) over (1:2.5.2-3build1) ... 82s Setting up libattr1:amd64 (1:2.5.2-3build2) ... 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 ... 83957 files and directories currently installed.) 82s Preparing to unpack .../00-mawk_1.3.4.20260129-1_amd64.deb ... 82s Unpacking mawk (1.3.4.20260129-1) over (1.3.4.20250131-2) ... 82s Preparing to unpack .../01-libdevmapper1.02.1_2%3a1.02.205-2ubuntu3_amd64.deb ... 82s Unpacking libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) over (2:1.02.205-2ubuntu2) ... 82s Preparing to unpack .../02-dmsetup_2%3a1.02.205-2ubuntu3_amd64.deb ... 82s Unpacking dmsetup (2:1.02.205-2ubuntu3) over (2:1.02.205-2ubuntu2) ... 82s Preparing to unpack .../03-less_668-1build1_amd64.deb ... 82s Unpacking less (668-1build1) over (668-1) ... 82s Preparing to unpack .../04-libkeyutils1_1.6.3-6ubuntu3_amd64.deb ... 82s Unpacking libkeyutils1:amd64 (1.6.3-6ubuntu3) over (1.6.3-6ubuntu2) ... 82s Preparing to unpack .../05-python3-linkify-it_2.0.3-1ubuntu3_all.deb ... 82s Unpacking python3-linkify-it (2.0.3-1ubuntu3) over (2.0.3-1ubuntu2) ... 82s Preparing to unpack .../06-python3-markdown-it_3.0.0-3build1_all.deb ... 82s Unpacking python3-markdown-it (3.0.0-3build1) over (3.0.0-3) ... 82s Preparing to unpack .../07-busybox-static_1%3a1.37.0-7ubuntu1_amd64.deb ... 82s Unpacking busybox-static (1:1.37.0-7ubuntu1) over (1:1.37.0-4ubuntu1) ... 82s Preparing to unpack .../08-libdrm-common_2.4.131-1_all.deb ... 82s Unpacking libdrm-common (2.4.131-1) over (2.4.129-1) ... 82s Preparing to unpack .../09-libdrm2_2.4.131-1_amd64.deb ... 82s Unpacking libdrm2:amd64 (2.4.131-1) over (2.4.129-1) ... 82s Preparing to unpack .../10-libgpm2_1.20.7-12build1_amd64.deb ... 82s Unpacking libgpm2:amd64 (1.20.7-12build1) over (1.20.7-12) ... 82s Preparing to unpack .../11-libmaxminddb0_1.12.2-1build2_amd64.deb ... 82s Unpacking libmaxminddb0:amd64 (1.12.2-1build2) over (1.12.2-1build1) ... 82s Preparing to unpack .../12-libsensors-config_1%3a3.6.2-2build1_all.deb ... 82s Unpacking libsensors-config (1:3.6.2-2build1) over (1:3.6.2-2) ... 82s Preparing to unpack .../13-libsensors5_1%3a3.6.2-2build1_amd64.deb ... 83s Unpacking libsensors5:amd64 (1:3.6.2-2build1) over (1:3.6.2-2) ... 83s Preparing to unpack .../14-busybox-initramfs_1%3a1.37.0-7ubuntu1_amd64.deb ... 83s Unpacking busybox-initramfs (1:1.37.0-7ubuntu1) over (1:1.37.0-4ubuntu1) ... 83s Preparing to unpack .../15-libdrm-amdgpu1_2.4.131-1_amd64.deb ... 83s Unpacking libdrm-amdgpu1:amd64 (2.4.131-1) over (2.4.129-1) ... 83s Preparing to unpack .../16-libnpth0t64_1.8-3build1_amd64.deb ... 83s Unpacking libnpth0t64:amd64 (1.8-3build1) over (1.8-3) ... 83s Preparing to unpack .../17-patch_2.8-2build1_amd64.deb ... 83s Unpacking patch (2.8-2build1) over (2.8-2) ... 83s Preparing to unpack .../18-pollinate_4.33-4ubuntu5_all.deb ... 83s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ... 83s Preparing to unpack .../19-python3-jinja2_3.1.6-1build1_all.deb ... 83s Unpacking python3-jinja2 (3.1.6-1build1) over (3.1.6-1) ... 83s Preparing to unpack .../20-python3-referencing_0.36.2-1ubuntu2_all.deb ... 83s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ... 83s Preparing to unpack .../21-amd64-microcode_3.20251202.1ubuntu1_amd64.deb ... 83s Unpacking amd64-microcode (3.20251202.1ubuntu1) over (3.20250708.1ubuntu1) ... 83s Setting up libnpth0t64:amd64 (1.8-3build1) ... 83s Setting up libkeyutils1:amd64 (1.6.3-6ubuntu3) ... 83s Setting up libgpm2:amd64 (1.20.7-12build1) ... 83s Setting up libmaxminddb0:amd64 (1.12.2-1build2) ... 83s Setting up libsensors-config (1:3.6.2-2build1) ... 83s Setting up less (668-1build1) ... 83s Setting up amd64-microcode (3.20251202.1ubuntu1) ... 83s amd64-microcode: microcode will be updated at next boot 83s Setting up python3-jinja2 (3.1.6-1build1) ... 83s Setting up pollinate (4.33-4ubuntu5) ... 93s Setting up busybox-static (1:1.37.0-7ubuntu1) ... 93s Setting up patch (2.8-2build1) ... 93s Setting up libsensors5:amd64 (1:3.6.2-2build1) ... 93s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ... 93s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ... 93s Setting up dmsetup (2:1.02.205-2ubuntu3) ... 93s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 94s Setting up mawk (1.3.4.20260129-1) ... 94s Setting up libdrm-common (2.4.131-1) ... 94s Setting up python3-referencing (0.36.2-1ubuntu2) ... 94s Setting up python3-markdown-it (3.0.0-3build1) ... 94s Setting up libdrm2:amd64 (2.4.131-1) ... 94s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... 94s Processing triggers for libc-bin (2.42-2ubuntu4) ... 94s Processing triggers for man-db (2.13.1-1) ... 95s Processing triggers for install-info (7.2-5) ... 95s Processing triggers for initramfs-tools (0.150ubuntu7) ... 95s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 99s autopkgtest [10:26:16]: upgrading testbed (apt dist-upgrade and autopurge) 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s Calculating upgrade... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s Solving dependencies... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s autopkgtest [10:26:18]: rebooting testbed after setup commands that affected boot 129s autopkgtest [10:26:46]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:49:02 UTC 2026 132s autopkgtest [10:26:49]: @@@@@@@@@@@@@@@@@@@@ apt-source pycoqc 140s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (dsc) [2027 B] 140s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (tar) [41.6 MB] 140s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (diff) [6840 B] 140s gpgv: Signature made Sat Jan 18 02:09:23 2025 UTC 140s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 140s gpgv: issuer "tchet@debian.org" 140s gpgv: Can't check signature: No public key 140s dpkg-source: warning: cannot verify inline signature for ./pycoqc_2.5.2+dfsg-4.dsc: no acceptable signature found 141s autopkgtest [10:26:58]: testing package pycoqc version 2.5.2+dfsg-4 141s autopkgtest [10:26:58]: build not needed 146s autopkgtest [10:27:03]: test run-unit-test: preparing testbed 146s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Solving dependencies... 147s The following NEW packages will be installed: 147s libblas3 libdeflate0 libgfortran5 libhdf5-310 libhdf5-hl-310 libhts3t64 147s libhtscodecs2 liblapack3 liblzf1 libqhull-r8.0 libsz2 pycoqc 147s python3-decorator python3-fastjsonschema python3-h5py python3-h5py-serial 147s python3-jupyter-core python3-nbformat python3-numpy python3-numpy-dev 147s python3-pandas python3-pandas-lib python3-platformdirs python3-plotly 147s python3-pysam python3-pytz python3-scipy python3-tenacity python3-tqdm 147s python3-traitlets 147s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 147s Need to get 52.7 MB of archives. 147s After this operation, 336 MB of additional disk space will be used. 147s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-3 [147 kB] 147s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 147s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-12ubuntu1 [939 kB] 147s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 148s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.3.5+ds-3 [8129 kB] 149s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 149s Get:7 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsz2 amd64 1.1.5-1 [17.9 kB] 149s Get:8 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-310 amd64 1.14.6+repack-2 [1433 kB] 149s Get:9 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-hl-310 amd64 1.14.6+repack-2 [59.9 kB] 149s Get:10 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2build1 [108 kB] 149s Get:11 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.22.1+ds2-1 [461 kB] 149s Get:12 http://ftpmaster.internal/ubuntu resolute/universe amd64 liblzf1 amd64 3.6-4build1 [7490 B] 149s Get:13 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-8 [197 kB] 149s Get:14 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-h5py-serial amd64 3.15.1-4 [1586 kB] 149s Get:15 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-h5py all 3.15.1-4 [11.3 kB] 149s Get:16 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytz all 2025.2-5 [32.4 kB] 149s Get:17 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.3.3+dfsg-3 [6929 kB] 151s Get:18 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.3.3+dfsg-3 [2948 kB] 152s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-decorator all 5.2.1-2 [28.1 kB] 152s Get:20 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fastjsonschema all 2.21.1-1 [20.4 kB] 152s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-platformdirs all 4.5.1-1 [17.1 kB] 152s Get:22 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-traitlets all 5.14.3+really5.14.3-2 [71.7 kB] 152s Get:23 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-jupyter-core all 5.9.1-1 [28.9 kB] 152s Get:24 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-nbformat all 5.10.4-1 [39.2 kB] 152s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-tenacity all 9.0.0-0ubuntu1 [17.0 kB] 152s Get:26 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-plotly all 5.20.0+dfsg-1.1 [2766 kB] 153s Get:27 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pysam amd64 0.23.3+ds-2 [4536 kB] 154s Get:28 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-scipy amd64 1.16.3-4 [19.0 MB] 158s Get:29 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-tqdm all 4.67.1-7 [93.3 kB] 158s Get:30 http://ftpmaster.internal/ubuntu resolute/universe amd64 pycoqc all 2.5.2+dfsg-4 [36.4 kB] 158s Fetched 52.7 MB in 11s (4903 kB/s) 158s Selecting previously unselected package python3-numpy-dev:amd64. 158s (Reading database ... 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170s Setting up pycoqc (2.5.2+dfsg-4) ... 170s Processing triggers for libc-bin (2.42-2ubuntu4) ... 170s Processing triggers for man-db (2.13.1-1) ... 172s autopkgtest [10:27:29]: test run-unit-test: [----------------------- 172s Test 1 173s Checking arguments values 173s Check input data files 173s Parse data files 173s Merge data 173s Cleaning data 173s Loading plotting interface 173s PASS 173s 173s Test 2 174s Checking arguments values 174s Check input data files 174s Parse data files 174s Merge data 174s Cleaning data 174s Loading plotting interface 174s PASS 174s 174s Test 3 174s Checking arguments values 174s Check input data files 174s Parse data files 175s Merge data 175s Cleaning data 175s Loading plotting interface 175s PASS 175s 175s Test 4 175s Checking arguments values 175s Check input data files 175s Parse data files 175s Merge data 175s Cleaning data 176s Loading plotting interface 176s PASS 176s 176s Test 5 176s Checking arguments values 176s Check input data files 176s Parse data files 176s Merge data 176s Cleaning data 176s Loading plotting interface 177s PASS 177s 177s Test 6 177s PASS 177s 177s Test 7 178s Checking arguments values 178s Check input data files 178s Parse data files 178s Merge data 178s Cleaning data 178s Loading plotting interface 178s PASS 178s 178s Test 8 179s 0 reads [00:00, ? reads/s] 22 reads [00:00, 2987.30 reads/s] 179s Total reads: 22 / Average speed: 1253.1 reads/s 179s 179s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template 179s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out 179s 3e81c32a-f2ee-4719-a88d-e0affe93d26f 40ebe55356ada6c830fa793745ef4c498d896c73 348 24 1137 8.124 filtered_out 179s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out 179s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out 179s 6af04302-04c8-4d8d-8e87-aa69178b3f24 40ebe55356ada6c830fa793745ef4c498d896c73 36 26 832 8.234 filtered_out 179s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out 179s 3f09025f-3d2c-4f84-9ea6-63dba736b649 40ebe55356ada6c830fa793745ef4c498d896c73 418 17 593 7.742 filtered_out 179s 4e21bf07-e2df-42d8-b347-59ef2c0618ea 40ebe55356ada6c830fa793745ef4c498d896c73 290 31 1160 8.741 filtered_out 179s 9a1c5296-2ab1-4abd-8d50-e059754cf332 40ebe55356ada6c830fa793745ef4c498d896c73 319 33 1235 8.119 filtered_out 179s PASS 179s 179s Test 9 179s Check input data and options 179s Start processing fast5 files 179s 0 reads [00:00, ? reads/s] 22 reads [00:00, 1868.40 reads/s] 179s Overall counts valid files: 22 179s 179s fields found mean_qscore_template: 22 179s called_events: 22 179s duration: 22 179s strand_score: 22 179s 179s fields not found 179s Total reads: 22 / Average speed: 1210.37 reads/s 179s 179s mean_qscore_template called_events duration strand_score 179s 8.124 2978 44675 -0.0005 179s 8.304 1547 23218 -0.0008 179s 7.805 1438 21583 -0.0006 179s 8.234 1827 27409 -0.0011 179s 8.23 2778 51387 -0.0007 179s 8.56 5838 87570 -0.0003 179s 7.742 2142 32138 -0.0004 179s 8.119 3181 47720 -0.0004 179s 8.741 3117 46767 -0.0006 179s PASS 179s 179s Test 10 180s Check input data and options 180s Start processing fast5 files 180s 0 reads [00:00, ? reads/s] 22 reads [00:00, 2160.85 reads/s] 180s Overall counts valid files: 22 180s 180s fields found read_id: 22 180s run_id: 22 180s channel: 22 180s start_time: 22 180s sequence_length_template: 22 180s mean_qscore_template: 22 180s calibration_strand_genome_template: 22 180s 180s fields not found barcode_arrangement: 22 180s 180s Total reads: 22 / Average speed: 1097.44 reads/s 180s 180s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template path 180s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out /tmp/autopkgtest.WPlDkt/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_318_strand.fast5 180s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out /tmp/autopkgtest.WPlDkt/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_121_strand.fast5 180s 6af04302-04c8-4d8d-8e87-aa69178b3f24 40ebe55356ada6c830fa793745ef4c498d896c73 36 26 832 8.234 filtered_out /tmp/autopkgtest.WPlDkt/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_36_strand.fast5 180s 3e81c32a-f2ee-4719-a88d-e0affe93d26f 40ebe55356ada6c830fa793745ef4c498d896c73 348 24 1137 8.124 filtered_out /tmp/autopkgtest.WPlDkt/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_348_strand.fast5 180s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out /tmp/autopkgtest.WPlDkt/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_191_strand.fast5 180s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out /tmp/autopkgtest.WPlDkt/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_103_strand.fast5 180s 4e21bf07-e2df-42d8-b347-59ef2c0618ea 40ebe55356ada6c830fa793745ef4c498d896c73 290 31 1160 8.741 filtered_out /tmp/autopkgtest.WPlDkt/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_290_strand.fast5 180s 3f09025f-3d2c-4f84-9ea6-63dba736b649 40ebe55356ada6c830fa793745ef4c498d896c73 418 17 593 7.742 filtered_out /tmp/autopkgtest.WPlDkt/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_418_strand.fast5 180s bcb20156-a5fe-4daa-aad9-b62c286e468d 40ebe55356ada6c830fa793745ef4c498d896c73 192 21 306 7.337 filtered_out /tmp/autopkgtest.WPlDkt/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_192_strand.fast5 180s PASS 180s 180s Test 11 180s Import data from sequencing summary file(s) and cleanup 180s Read files and import in a dataframe 180s Check input data files 180s Parse data files 180s Merge data 180s Cleanup missing barcodes values 180s Cleaning up low frequency barcodes 180s Split data per barcode 180s Processing data for Barcode barcode02 180s Processing data for Barcode barcode07 180s Processing data for Barcode barcode08 180s Processing data for Barcode barcode09 180s Processing data for Barcode barcode10 181s Processing data for Barcode barcode11 181s Processing data for Barcode barcode12 181s Processing data for Barcode unclassified 181s Barcode Counts 181s Counts Write 181s barcode02 2 False 181s barcode07 1 False 181s barcode08 30 False 181s barcode09 9945 True 181s barcode10 12644 True 181s barcode11 13594 True 181s barcode12 9813 True 181s unclassified 3971 False 181s PASS 181s 181s Test 12 181s General info 181s package_name: pycoQC 181s package_version: 2.5.2 181s timestamp: 2026-02-06 10:27:38.747373 181s 181s Runtime options 181s summary_file: ['Guppy-basecall-1D-DNA_sequencing_summary.txt'] 181s barcode_file: ['Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt'] 181s output_dir: results/ 181s output_unclassified: False 181s min_barcode_percent: 0.1 181s verbose: True 181s quiet: False 181s 181s Import data from sequencing summary file(s) and cleanup 181s Read files and import in a dataframe 181s Check input data files 181s Sequencing summary files found: Guppy-basecall-1D-DNA_sequencing_summary.txt 181s Barcode files found: Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt 181s Parse data files 181s Parse summary files 181s 3,999 reads found in initial file 181s Parse barcode files 181s Found valid Deepbinner barcode file 181s 3,775 reads with barcodes assigned 181s Merge data 181s Cleanup missing barcodes values 181s Cleaning up low frequency barcodes 181s Split data per barcode 181s Processing data for Barcode 1 181s Processing data for Barcode 2 181s Processing data for Barcode 3 181s Processing data for Barcode 4 181s Processing data for Barcode 5 181s Processing data for Barcode 6 181s Processing data for Barcode 7 181s Processing data for Barcode 8 181s Processing data for Barcode unclassified 181s Barcode Counts 181s Counts Write 181s 1 534 True 181s 2 206 True 181s 3 562 True 181s 4 579 True 181s 5 590 True 181s 6 655 True 181s 7 271 True 181s 8 378 True 181s unclassified 224 False 181s PASS 181s 181s Check if files really exist 181s PASS 181s 182s autopkgtest [10:27:39]: test run-unit-test: -----------------------] 182s run-unit-test PASS 182s autopkgtest [10:27:39]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 182s autopkgtest [10:27:39]: @@@@@@@@@@@@@@@@@@@@ summary 182s run-unit-test PASS