0s autopkgtest [08:21:34]: starting date and time: 2025-01-08 08:21:34+0000 0s autopkgtest [08:21:34]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [08:21:34]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.11g8g5f_/out --timeout-copy=6000 --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=jinja2/3.1.3-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-ppc64el-14.secgroup --name adt-plucky-ppc64el-pycoqc-20250108-071129-juju-7f2275-prod-proposed-migration-environment-20-876e713d-7ce0-44ab-9edd-db8b9b82c7a2 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 112s autopkgtest [08:23:26]: testbed dpkg architecture: ppc64el 112s autopkgtest [08:23:26]: testbed apt version: 2.9.18 112s autopkgtest [08:23:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 112s autopkgtest [08:23:26]: testbed release detected to be: None 113s autopkgtest [08:23:27]: updating testbed package index (apt update) 113s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 114s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 114s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 114s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 114s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 114s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [129 kB] 114s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.3 kB] 114s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [818 kB] 114s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [243 kB] 114s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted ppc64el Packages [756 B] 114s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [989 kB] 114s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [15.8 kB] 114s Fetched 2297 kB in 1s (2175 kB/s) 115s Reading package lists... 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Calculating upgrade... 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 117s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 117s autopkgtest [08:23:31]: upgrading testbed (apt dist-upgrade and autopurge) 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 117s Starting 2 pkgProblemResolver with broken count: 0 117s Done 118s Entering ResolveByKeep 118s 118s The following packages will be upgraded: 118s python3-jinja2 118s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s Need to get 108 kB of archives. 118s After this operation, 0 B of additional disk space will be used. 118s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-jinja2 all 3.1.3-2 [108 kB] 119s Fetched 108 kB in 0s (318 kB/s) 119s (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 ... 74025 files and directories currently installed.) 119s Preparing to unpack .../python3-jinja2_3.1.3-2_all.deb ... 119s Unpacking python3-jinja2 (3.1.3-2) over (3.1.3-1.1) ... 119s Setting up python3-jinja2 (3.1.3-2) ... 119s Reading package lists... 120s Building dependency tree... 120s Reading state information... 120s Starting pkgProblemResolver with broken count: 0 120s Starting 2 pkgProblemResolver with broken count: 0 120s Done 120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s autopkgtest [08:23:36]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 123s autopkgtest [08:23:37]: @@@@@@@@@@@@@@@@@@@@ apt-source pycoqc 126s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pycoqc 2.5.2+dfsg-3 (dsc) [2051 B] 126s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pycoqc 2.5.2+dfsg-3 (tar) [41.6 MB] 126s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pycoqc 2.5.2+dfsg-3 (diff) [6764 B] 126s gpgv: Signature made Tue Dec 7 15:51:27 2021 UTC 126s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 126s gpgv: issuer "tille@debian.org" 126s gpgv: Can't check signature: No public key 126s dpkg-source: warning: cannot verify inline signature for ./pycoqc_2.5.2+dfsg-3.dsc: no acceptable signature found 128s autopkgtest [08:23:42]: testing package pycoqc version 2.5.2+dfsg-3 128s autopkgtest [08:23:42]: build not needed 132s autopkgtest [08:23:46]: test run-unit-test: preparing testbed 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 133s Starting pkgProblemResolver with broken count: 0 133s Starting 2 pkgProblemResolver with broken count: 0 133s Done 133s The following NEW packages will be installed: 133s libaec0 libblas3 libdeflate0 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 133s libhts3t64 libhtscodecs2 liblapack3 liblbfgsb0 liblzf1 libsz2 pycoqc 133s python3-dateutil python3-decorator python3-fastjsonschema python3-h5py 133s python3-h5py-serial python3-jupyter-core python3-nbformat python3-numpy 133s python3-pandas python3-pandas-lib python3-platformdirs python3-plotly 133s python3-pysam python3-scipy python3-tenacity python3-tqdm python3-traitlets 133s python3-tz 133s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 133s Need to get 53.2 MB of archives. 133s After this operation, 380 MB of additional disk space will be used. 133s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libaec0 ppc64el 1.1.3-1 [30.1 kB] 134s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-4 [222 kB] 134s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.22-1 [63.3 kB] 134s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-12ubuntu1 [571 kB] 134s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libsz2 ppc64el 1.1.3-1 [5566 B] 134s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-5ubuntu1 [1394 kB] 134s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-hl-100t64 ppc64el 1.10.10+repack-5ubuntu1 [71.2 kB] 134s Get:8 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhtscodecs2 ppc64el 1.6.1-1 [113 kB] 134s Get:9 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhts3t64 ppc64el 1.20+ds-2 [574 kB] 134s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-4 [2814 kB] 134s Get:11 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 134s Get:12 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 134s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-12 [4917 kB] 134s Get:14 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py-serial ppc64el 3.11.0-8ubuntu3 [1598 kB] 134s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dateutil all 2.9.0-3 [80.2 kB] 134s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tz all 2024.2-1 [31.5 kB] 134s Get:17 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas-lib ppc64el 2.2.3+dfsg-5ubuntu1 [7350 kB] 135s Get:18 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 135s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 135s Get:20 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fastjsonschema all 2.21.1-1 [20.4 kB] 135s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-platformdirs all 4.3.6-1 [16.8 kB] 135s Get:22 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 135s Get:23 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-jupyter-core all 5.7.2-5 [28.1 kB] 135s Get:24 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-nbformat all 5.9.1-1 [41.2 kB] 135s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tenacity all 8.5.0-0ubuntu1 [17.0 kB] 135s Get:26 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-plotly all 5.20.0+dfsg-1 [2766 kB] 135s Get:27 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pysam ppc64el 0.22.1+ds-2build1 [4445 kB] 135s Get:28 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.14.1-3ubuntu1 [22.6 MB] 135s Get:29 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-tqdm all 4.67.1-1 [92.5 kB] 135s Get:30 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py all 3.11.0-8ubuntu3 [7982 B] 135s Get:31 http://ftpmaster.internal/ubuntu plucky/universe ppc64el pycoqc all 2.5.2+dfsg-3 [36.4 kB] 136s Fetched 53.2 MB in 2s (25.4 MB/s) 136s Selecting previously unselected package libaec0:ppc64el. 136s (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 ... 74025 files and directories currently installed.) 136s Preparing to unpack .../00-libaec0_1.1.3-1_ppc64el.deb ... 136s Unpacking libaec0:ppc64el (1.1.3-1) ... 136s Selecting previously unselected package libblas3:ppc64el. 136s Preparing to unpack .../01-libblas3_3.12.0-4_ppc64el.deb ... 136s Unpacking libblas3:ppc64el (3.12.0-4) ... 136s Selecting previously unselected package libdeflate0:ppc64el. 136s Preparing to unpack .../02-libdeflate0_1.22-1_ppc64el.deb ... 136s Unpacking libdeflate0:ppc64el (1.22-1) ... 136s Selecting previously unselected package libgfortran5:ppc64el. 136s Preparing to unpack .../03-libgfortran5_14.2.0-12ubuntu1_ppc64el.deb ... 136s Unpacking libgfortran5:ppc64el (14.2.0-12ubuntu1) ... 136s Selecting previously unselected package libsz2:ppc64el. 136s Preparing to unpack .../04-libsz2_1.1.3-1_ppc64el.deb ... 136s Unpacking libsz2:ppc64el (1.1.3-1) ... 136s Selecting previously unselected package libhdf5-103-1t64:ppc64el. 136s Preparing to unpack .../05-libhdf5-103-1t64_1.10.10+repack-5ubuntu1_ppc64el.deb ... 136s Unpacking libhdf5-103-1t64:ppc64el (1.10.10+repack-5ubuntu1) ... 136s Selecting previously unselected package libhdf5-hl-100t64:ppc64el. 136s Preparing to unpack .../06-libhdf5-hl-100t64_1.10.10+repack-5ubuntu1_ppc64el.deb ... 136s Unpacking libhdf5-hl-100t64:ppc64el (1.10.10+repack-5ubuntu1) ... 136s Selecting previously unselected package libhtscodecs2:ppc64el. 136s Preparing to unpack .../07-libhtscodecs2_1.6.1-1_ppc64el.deb ... 136s Unpacking libhtscodecs2:ppc64el (1.6.1-1) ... 136s Selecting previously unselected package libhts3t64:ppc64el. 136s Preparing to unpack .../08-libhts3t64_1.20+ds-2_ppc64el.deb ... 136s Unpacking libhts3t64:ppc64el (1.20+ds-2) ... 136s Selecting previously unselected package liblapack3:ppc64el. 136s Preparing to unpack .../09-liblapack3_3.12.0-4_ppc64el.deb ... 136s Unpacking liblapack3:ppc64el (3.12.0-4) ... 136s Selecting previously unselected package liblbfgsb0:ppc64el. 136s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 136s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 136s Selecting previously unselected package liblzf1:ppc64el. 136s Preparing to unpack .../11-liblzf1_3.6-4_ppc64el.deb ... 136s Unpacking liblzf1:ppc64el (3.6-4) ... 136s Selecting previously unselected package python3-numpy. 136s Preparing to unpack .../12-python3-numpy_1%3a1.26.4+ds-12_ppc64el.deb ... 136s Unpacking python3-numpy (1:1.26.4+ds-12) ... 136s Selecting previously unselected package python3-h5py-serial. 136s Preparing to unpack .../13-python3-h5py-serial_3.11.0-8ubuntu3_ppc64el.deb ... 136s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 136s Selecting previously unselected package python3-dateutil. 136s Preparing to unpack .../14-python3-dateutil_2.9.0-3_all.deb ... 136s Unpacking python3-dateutil (2.9.0-3) ... 136s Selecting previously unselected package python3-tz. 136s Preparing to unpack .../15-python3-tz_2024.2-1_all.deb ... 136s Unpacking python3-tz (2024.2-1) ... 136s Selecting previously unselected package python3-pandas-lib:ppc64el. 136s Preparing to unpack .../16-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_ppc64el.deb ... 136s Unpacking python3-pandas-lib:ppc64el (2.2.3+dfsg-5ubuntu1) ... 137s Selecting previously unselected package python3-pandas. 137s Preparing to unpack .../17-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 137s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 137s Selecting previously unselected package python3-decorator. 137s Preparing to unpack .../18-python3-decorator_5.1.1-5_all.deb ... 137s Unpacking python3-decorator (5.1.1-5) ... 137s Selecting previously unselected package python3-fastjsonschema. 137s Preparing to unpack .../19-python3-fastjsonschema_2.21.1-1_all.deb ... 137s Unpacking python3-fastjsonschema (2.21.1-1) ... 137s Selecting previously unselected package python3-platformdirs. 137s Preparing to unpack .../20-python3-platformdirs_4.3.6-1_all.deb ... 137s Unpacking python3-platformdirs (4.3.6-1) ... 137s Selecting previously unselected package python3-traitlets. 137s Preparing to unpack .../21-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 137s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 137s Selecting previously unselected package python3-jupyter-core. 137s Preparing to unpack .../22-python3-jupyter-core_5.7.2-5_all.deb ... 137s Unpacking python3-jupyter-core (5.7.2-5) ... 137s Selecting previously unselected package python3-nbformat. 137s Preparing to unpack .../23-python3-nbformat_5.9.1-1_all.deb ... 137s Unpacking python3-nbformat (5.9.1-1) ... 137s Selecting previously unselected package python3-tenacity. 137s Preparing to unpack .../24-python3-tenacity_8.5.0-0ubuntu1_all.deb ... 137s Unpacking python3-tenacity (8.5.0-0ubuntu1) ... 137s Selecting previously unselected package python3-plotly. 137s Preparing to unpack .../25-python3-plotly_5.20.0+dfsg-1_all.deb ... 137s Unpacking python3-plotly (5.20.0+dfsg-1) ... 138s Selecting previously unselected package python3-pysam. 138s Preparing to unpack .../26-python3-pysam_0.22.1+ds-2build1_ppc64el.deb ... 138s Unpacking python3-pysam (0.22.1+ds-2build1) ... 139s Selecting previously unselected package python3-scipy. 139s Preparing to unpack .../27-python3-scipy_1.14.1-3ubuntu1_ppc64el.deb ... 139s Unpacking python3-scipy (1.14.1-3ubuntu1) ... 139s Selecting previously unselected package python3-tqdm. 139s Preparing to unpack .../28-python3-tqdm_4.67.1-1_all.deb ... 139s Unpacking python3-tqdm (4.67.1-1) ... 139s Selecting previously unselected package python3-h5py. 139s Preparing to unpack .../29-python3-h5py_3.11.0-8ubuntu3_all.deb ... 139s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 139s Selecting previously unselected package pycoqc. 139s Preparing to unpack .../30-pycoqc_2.5.2+dfsg-3_all.deb ... 139s Unpacking pycoqc (2.5.2+dfsg-3) ... 139s Setting up libhtscodecs2:ppc64el (1.6.1-1) ... 139s Setting up python3-tenacity (8.5.0-0ubuntu1) ... 139s Setting up python3-tqdm (4.67.1-1) ... 140s Setting up libdeflate0:ppc64el (1.22-1) ... 140s Setting up libaec0:ppc64el (1.1.3-1) ... 140s Setting up python3-platformdirs (4.3.6-1) ... 140s Setting up python3-tz (2024.2-1) ... 140s Setting up python3-decorator (5.1.1-5) ... 140s Setting up libblas3:ppc64el (3.12.0-4) ... 140s 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 140s Setting up liblzf1:ppc64el (3.6-4) ... 140s Setting up libgfortran5:ppc64el (14.2.0-12ubuntu1) ... 140s Setting up python3-fastjsonschema (2.21.1-1) ... 140s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 140s Setting up libhts3t64:ppc64el (1.20+ds-2) ... 140s Setting up python3-dateutil (2.9.0-3) ... 140s Setting up python3-jupyter-core (5.7.2-5) ... 140s Setting up libsz2:ppc64el (1.1.3-1) ... 140s Setting up liblapack3:ppc64el (3.12.0-4) ... 140s 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 140s Setting up python3-pysam (0.22.1+ds-2build1) ... 141s Setting up python3-nbformat (5.9.1-1) ... 141s Setting up python3-plotly (5.20.0+dfsg-1) ... 148s Setting up python3-numpy (1:1.26.4+ds-12) ... 150s Setting up libhdf5-103-1t64:ppc64el (1.10.10+repack-5ubuntu1) ... 150s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 150s Setting up libhdf5-hl-100t64:ppc64el (1.10.10+repack-5ubuntu1) ... 150s Setting up python3-scipy (1.14.1-3ubuntu1) ... 154s Setting up python3-pandas-lib:ppc64el (2.2.3+dfsg-5ubuntu1) ... 154s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 154s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 159s Setting up python3-h5py (3.11.0-8ubuntu3) ... 159s Setting up pycoqc (2.5.2+dfsg-3) ... 160s Processing triggers for libc-bin (2.40-4ubuntu1) ... 160s Processing triggers for man-db (2.13.0-1) ... 161s autopkgtest [08:24:15]: test run-unit-test: [----------------------- 162s Test 1 163s Checking arguments values 163s Check input data files 163s Parse data files 163s Merge data 163s Cleaning data 163s Loading plotting interface 164s PASS 164s 164s Test 2 164s Checking arguments values 164s Check input data files 164s Parse data files 164s Merge data 164s Cleaning data 164s Loading plotting interface 165s PASS 165s 165s Test 3 166s Checking arguments values 166s Check input data files 166s Parse data files 166s Merge data 166s Cleaning data 166s Loading plotting interface 166s PASS 166s 166s Test 4 167s Checking arguments values 167s Check input data files 167s Parse data files 167s Merge data 167s Cleaning data 167s Loading plotting interface 168s PASS 168s 168s Test 5 169s Checking arguments values 169s Check input data files 169s Parse data files 169s Merge data 169s Cleaning data 169s Loading plotting interface 169s PASS 169s 169s Test 6 170s PASS 170s 170s Test 7 171s Checking arguments values 171s Check input data files 171s Parse data files 171s Merge data 171s Cleaning data 171s Loading plotting interface 171s PASS 171s 171s Test 8 172s 0 reads [00:00, ? reads/s] 22 reads [00:00, 722.96 reads/s] 172s Total reads: 22 / Average speed: 501.84 reads/s 172s 172s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template 172s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out 172s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out 172s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out 172s c38cbad9-d91e-4208-9317-832f4e2cc289 40ebe55356ada6c830fa793745ef4c498d896c73 113 30 824 8.693 filtered_out 172s f8325de9-a77e-4616-a4a8-69ecf32e1688 40ebe55356ada6c830fa793745ef4c498d896c73 354 16 568 8.206 filtered_out 172s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out 172s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out 172s 4e21bf07-e2df-42d8-b347-59ef2c0618ea 40ebe55356ada6c830fa793745ef4c498d896c73 290 31 1160 8.741 filtered_out 172s 6f4fffe7-ca07-4c5e-9ad1-7470f370a8b0 40ebe55356ada6c830fa793745ef4c498d896c73 301 16 553 7.881 filtered_out 172s PASS 172s 172s Test 9 173s Check input data and options 173s Start processing fast5 files 173s 0 reads [00:00, ? reads/s] 22 reads [00:00, 1290.48 reads/s] 173s Overall counts valid files: 22 173s 173s fields found mean_qscore_template: 22 173s called_events: 22 173s duration: 22 173s strand_score: 22 173s 173s fields not found 173s Total reads: 22 / Average speed: 781.01 reads/s 173s 173s mean_qscore_template called_events duration strand_score 173s 8.56 5838 87570 -0.0003 173s 8.23 2778 51387 -0.0007 173s 9.407 2848 42730 -0.0003 173s 7.805 1438 21583 -0.0006 173s 8.693 2383 35752 -0.0005 173s 8.206 1649 24747 -0.0009 173s 8.304 1547 23218 -0.0008 173s 8.741 3117 46767 -0.0006 173s 7.881 1513 24541 -0.0007 173s PASS 173s 173s Test 10 173s Check input data and options 173s Start processing fast5 files 174s 0 reads [00:00, ? reads/s] 22 reads [00:00, 839.18 reads/s] 174s Overall counts valid files: 22 174s 174s fields found read_id: 22 174s run_id: 22 174s channel: 22 174s start_time: 22 174s sequence_length_template: 22 174s mean_qscore_template: 22 174s calibration_strand_genome_template: 22 174s 174s fields not found barcode_arrangement: 22 174s 174s Total reads: 22 / Average speed: 597.03 reads/s 174s 174s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template path 174s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out /tmp/autopkgtest.faANWj/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_103_strand.fast5 174s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out /tmp/autopkgtest.faANWj/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_191_strand.fast5 174s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out /tmp/autopkgtest.faANWj/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_121_strand.fast5 174s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out /tmp/autopkgtest.faANWj/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_108_strand.fast5 174s c38cbad9-d91e-4208-9317-832f4e2cc289 40ebe55356ada6c830fa793745ef4c498d896c73 113 30 824 8.693 filtered_out /tmp/autopkgtest.faANWj/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_113_strand.fast5 174s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out /tmp/autopkgtest.faANWj/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_318_strand.fast5 174s f8325de9-a77e-4616-a4a8-69ecf32e1688 40ebe55356ada6c830fa793745ef4c498d896c73 354 16 568 8.206 filtered_out /tmp/autopkgtest.faANWj/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_354_strand.fast5 174s 6f4fffe7-ca07-4c5e-9ad1-7470f370a8b0 40ebe55356ada6c830fa793745ef4c498d896c73 301 16 553 7.881 filtered_out /tmp/autopkgtest.faANWj/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_301_strand.fast5 174s 5b7fadd0-c646-4c7b-9800-66ee658a5ca8 40ebe55356ada6c830fa793745ef4c498d896c73 150 37 468 7.608 filtered_out /tmp/autopkgtest.faANWj/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_150_strand.fast5 174s PASS 174s 174s Test 11 174s Import data from sequencing summary file(s) and cleanup 174s Read files and import in a dataframe 174s Check input data files 174s Parse data files 175s Merge data 175s Cleanup missing barcodes values 175s Cleaning up low frequency barcodes 175s Split data per barcode 175s Processing data for Barcode barcode02 175s Processing data for Barcode barcode07 175s Processing data for Barcode barcode08 175s Processing data for Barcode barcode09 175s Processing data for Barcode barcode10 175s Processing data for Barcode barcode11 175s Processing data for Barcode barcode12 175s Processing data for Barcode unclassified 175s Barcode Counts 175s Counts Write 175s barcode02 2 False 175s barcode07 1 False 175s barcode08 30 False 175s barcode09 9945 True 175s barcode10 12644 True 175s barcode11 13594 True 175s barcode12 9813 True 175s unclassified 3971 False 175s PASS 175s 175s Test 12 176s General info 176s package_name: pycoQC 176s package_version: 2.5.2 176s timestamp: 2025-01-08 08:24:30.396998 176s 176s Runtime options 176s summary_file: ['Guppy-basecall-1D-DNA_sequencing_summary.txt'] 176s barcode_file: ['Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt'] 176s output_dir: results/ 176s output_unclassified: False 176s min_barcode_percent: 0.1 176s verbose: True 176s quiet: False 176s 176s Import data from sequencing summary file(s) and cleanup 176s Read files and import in a dataframe 176s Check input data files 176s Sequencing summary files found: Guppy-basecall-1D-DNA_sequencing_summary.txt 176s Barcode files found: Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt 176s Parse data files 176s Parse summary files 176s 3,999 reads found in initial file 176s Parse barcode files 176s Found valid Deepbinner barcode file 176s 3,775 reads with barcodes assigned 176s Merge data 176s Cleanup missing barcodes values 176s Cleaning up low frequency barcodes 176s Split data per barcode 176s Processing data for Barcode 1 176s Processing data for Barcode 2 176s Processing data for Barcode 3 176s Processing data for Barcode 4 176s Processing data for Barcode 5 176s Processing data for Barcode 6 176s Processing data for Barcode 7 176s Processing data for Barcode 8 176s Processing data for Barcode unclassified 176s Barcode Counts 176s Counts Write 176s 1 534 True 176s 2 206 True 176s 3 562 True 176s 4 579 True 176s 5 590 True 176s 6 655 True 176s 7 271 True 176s 8 378 True 176s unclassified 224 False 176s PASS 176s 176s Check if files really exist 176s PASS 176s 176s autopkgtest [08:24:30]: test run-unit-test: -----------------------] 177s run-unit-test PASS 177s autopkgtest [08:24:31]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 177s autopkgtest [08:24:31]: @@@@@@@@@@@@@@@@@@@@ summary 177s run-unit-test PASS 194s nova [W] Using flock in prodstack6-ppc64el 194s flock: timeout while waiting to get lock 194s Creating nova instance adt-plucky-ppc64el-pycoqc-20250108-071129-juju-7f2275-prod-proposed-migration-environment-20-876e713d-7ce0-44ab-9edd-db8b9b82c7a2 from image adt/ubuntu-plucky-ppc64el-server-20250108.img (UUID 4336f050-c876-44a2-a40e-4862551c85cb)... 194s nova [W] Timed out waiting for 3f1dc4ca-9cfb-430d-997e-df52d6e666d1 to get deleted.