0s autopkgtest [07:09:39]: starting date and time: 2025-01-08 07:09:39+0000 0s autopkgtest [07:09:39]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [07:09:39]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.tpr83s9h/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-22.secgroup --name adt-plucky-arm64-pycoqc-20250108-070939-juju-7f2275-prod-proposed-migration-environment-20-0961f869-0bd4-407b-8d8b-5052f9be909e --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -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/ 162s autopkgtest [07:12:21]: testbed dpkg architecture: arm64 162s autopkgtest [07:12:21]: testbed apt version: 2.9.18 162s autopkgtest [07:12:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 163s autopkgtest [07:12:22]: testbed release detected to be: None 163s autopkgtest [07:12:22]: updating testbed package index (apt update) 164s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 164s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 164s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 164s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 164s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [18.0 kB] 164s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 164s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [830 kB] 164s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [129 kB] 164s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [258 kB] 164s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [57.8 kB] 164s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [980 kB] 164s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [23.3 kB] 165s Fetched 2380 kB in 1s (2429 kB/s) 166s Reading package lists... 166s Reading package lists... 167s Building dependency tree... 167s Reading state information... 167s Calculating upgrade... 168s The following packages will be upgraded: 168s nano 168s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 168s Need to get 289 kB of archives. 168s After this operation, 0 B of additional disk space will be used. 168s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 nano arm64 8.3-1 [289 kB] 169s Fetched 289 kB in 0s (706 kB/s) 169s (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 ... 80185 files and directories currently installed.) 169s Preparing to unpack .../archives/nano_8.3-1_arm64.deb ... 169s Unpacking nano (8.3-1) over (8.2-1) ... 169s Setting up nano (8.3-1) ... 169s Installing new version of config file /etc/nanorc ... 169s Processing triggers for man-db (2.13.0-1) ... 170s Processing triggers for install-info (7.1.1-1) ... 171s Reading package lists... 171s Building dependency tree... 171s Reading state information... 172s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 172s autopkgtest [07:12:31]: upgrading testbed (apt dist-upgrade and autopurge) 172s Reading package lists... 172s Building dependency tree... 172s Reading state information... 173s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 173s Starting 2 pkgProblemResolver with broken count: 0 173s Done 174s Entering ResolveByKeep 174s 175s The following packages will be upgraded: 175s python3-jinja2 175s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 175s Need to get 108 kB of archives. 175s After this operation, 0 B of additional disk space will be used. 175s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-jinja2 all 3.1.3-2 [108 kB] 175s Fetched 108 kB in 0s (297 kB/s) 175s (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 ... 80185 files and directories currently installed.) 175s Preparing to unpack .../python3-jinja2_3.1.3-2_all.deb ... 175s Unpacking python3-jinja2 (3.1.3-2) over (3.1.3-1.1) ... 176s Setting up python3-jinja2 (3.1.3-2) ... 176s Reading package lists... 176s Building dependency tree... 176s Reading state information... 177s Starting pkgProblemResolver with broken count: 0 177s Starting 2 pkgProblemResolver with broken count: 0 177s Done 178s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 181s autopkgtest [07:12:40]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 181s autopkgtest [07:12:40]: @@@@@@@@@@@@@@@@@@@@ apt-source pycoqc 184s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pycoqc 2.5.2+dfsg-3 (dsc) [2051 B] 184s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pycoqc 2.5.2+dfsg-3 (tar) [41.6 MB] 184s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pycoqc 2.5.2+dfsg-3 (diff) [6764 B] 184s gpgv: Signature made Tue Dec 7 15:51:27 2021 UTC 184s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 184s gpgv: issuer "tille@debian.org" 184s gpgv: Can't check signature: No public key 184s dpkg-source: warning: cannot verify inline signature for ./pycoqc_2.5.2+dfsg-3.dsc: no acceptable signature found 186s autopkgtest [07:12:45]: testing package pycoqc version 2.5.2+dfsg-3 186s autopkgtest [07:12:45]: build not needed 190s autopkgtest [07:12:49]: test run-unit-test: preparing testbed 190s Reading package lists... 191s Building dependency tree... 191s Reading state information... 191s Starting pkgProblemResolver with broken count: 0 191s Starting 2 pkgProblemResolver with broken count: 0 191s Done 192s The following NEW packages will be installed: 192s libaec0 libblas3 libdeflate0 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 192s libhts3t64 libhtscodecs2 liblapack3 liblbfgsb0 liblzf1 libsz2 pycoqc 192s python3-dateutil python3-decorator python3-fastjsonschema python3-h5py 192s python3-h5py-serial python3-jupyter-core python3-nbformat python3-numpy 192s python3-pandas python3-pandas-lib python3-platformdirs python3-plotly 192s python3-pysam python3-scipy python3-tenacity python3-tqdm python3-traitlets 192s python3-tz 192s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 192s Need to get 47.1 MB of archives. 192s After this operation, 312 MB of additional disk space will be used. 192s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 192s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-4 [152 kB] 192s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 192s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-12ubuntu1 [437 kB] 192s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 192s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-5ubuntu1 [1210 kB] 192s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-5ubuntu1 [56.9 kB] 192s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 192s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-2 [437 kB] 192s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-4 [2305 kB] 192s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 192s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 192s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [4153 kB] 193s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.11.0-8ubuntu3 [1452 kB] 193s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 193s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.2-1 [31.5 kB] 193s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5ubuntu1 [6921 kB] 193s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 193s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 193s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fastjsonschema all 2.21.1-1 [20.4 kB] 193s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 193s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 193s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jupyter-core all 5.7.2-5 [28.1 kB] 193s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-nbformat all 5.9.1-1 [41.2 kB] 193s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tenacity all 8.5.0-0ubuntu1 [17.0 kB] 193s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-plotly all 5.20.0+dfsg-1 [2766 kB] 193s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.22.1+ds-2build1 [3987 kB] 193s Get:28 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-3ubuntu1 [19.5 MB] 193s Get:29 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.67.1-1 [92.5 kB] 193s Get:30 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.11.0-8ubuntu3 [7982 B] 193s Get:31 http://ftpmaster.internal/ubuntu plucky/universe arm64 pycoqc all 2.5.2+dfsg-3 [36.4 kB] 194s Fetched 47.1 MB in 2s (26.2 MB/s) 194s Selecting previously unselected package libaec0:arm64. 194s (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 ... 80185 files and directories currently installed.) 194s Preparing to unpack .../00-libaec0_1.1.3-1_arm64.deb ... 194s Unpacking libaec0:arm64 (1.1.3-1) ... 194s Selecting previously unselected package libblas3:arm64. 194s Preparing to unpack .../01-libblas3_3.12.0-4_arm64.deb ... 194s Unpacking libblas3:arm64 (3.12.0-4) ... 194s Selecting previously unselected package libdeflate0:arm64. 194s Preparing to unpack .../02-libdeflate0_1.22-1_arm64.deb ... 194s Unpacking libdeflate0:arm64 (1.22-1) ... 194s Selecting previously unselected package libgfortran5:arm64. 194s Preparing to unpack .../03-libgfortran5_14.2.0-12ubuntu1_arm64.deb ... 194s Unpacking libgfortran5:arm64 (14.2.0-12ubuntu1) ... 194s Selecting previously unselected package libsz2:arm64. 194s Preparing to unpack .../04-libsz2_1.1.3-1_arm64.deb ... 194s Unpacking libsz2:arm64 (1.1.3-1) ... 194s Selecting previously unselected package libhdf5-103-1t64:arm64. 194s Preparing to unpack .../05-libhdf5-103-1t64_1.10.10+repack-5ubuntu1_arm64.deb ... 194s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-5ubuntu1) ... 194s Selecting previously unselected package libhdf5-hl-100t64:arm64. 194s Preparing to unpack .../06-libhdf5-hl-100t64_1.10.10+repack-5ubuntu1_arm64.deb ... 194s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-5ubuntu1) ... 194s Selecting previously unselected package libhtscodecs2:arm64. 194s Preparing to unpack .../07-libhtscodecs2_1.6.1-1_arm64.deb ... 194s Unpacking libhtscodecs2:arm64 (1.6.1-1) ... 194s Selecting previously unselected package libhts3t64:arm64. 194s Preparing to unpack .../08-libhts3t64_1.20+ds-2_arm64.deb ... 194s Unpacking libhts3t64:arm64 (1.20+ds-2) ... 194s Selecting previously unselected package liblapack3:arm64. 194s Preparing to unpack .../09-liblapack3_3.12.0-4_arm64.deb ... 194s Unpacking liblapack3:arm64 (3.12.0-4) ... 194s Selecting previously unselected package liblbfgsb0:arm64. 194s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 194s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 195s Selecting previously unselected package liblzf1:arm64. 195s Preparing to unpack .../11-liblzf1_3.6-4_arm64.deb ... 195s Unpacking liblzf1:arm64 (3.6-4) ... 195s Selecting previously unselected package python3-numpy. 195s Preparing to unpack .../12-python3-numpy_1%3a1.26.4+ds-12_arm64.deb ... 195s Unpacking python3-numpy (1:1.26.4+ds-12) ... 195s Selecting previously unselected package python3-h5py-serial. 195s Preparing to unpack .../13-python3-h5py-serial_3.11.0-8ubuntu3_arm64.deb ... 195s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 195s Selecting previously unselected package python3-dateutil. 195s Preparing to unpack .../14-python3-dateutil_2.9.0-3_all.deb ... 195s Unpacking python3-dateutil (2.9.0-3) ... 195s Selecting previously unselected package python3-tz. 195s Preparing to unpack .../15-python3-tz_2024.2-1_all.deb ... 195s Unpacking python3-tz (2024.2-1) ... 195s Selecting previously unselected package python3-pandas-lib:arm64. 195s Preparing to unpack .../16-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_arm64.deb ... 195s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5ubuntu1) ... 195s Selecting previously unselected package python3-pandas. 195s Preparing to unpack .../17-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 195s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 196s Selecting previously unselected package python3-decorator. 196s Preparing to unpack .../18-python3-decorator_5.1.1-5_all.deb ... 196s Unpacking python3-decorator (5.1.1-5) ... 196s Selecting previously unselected package python3-fastjsonschema. 196s Preparing to unpack .../19-python3-fastjsonschema_2.21.1-1_all.deb ... 196s Unpacking python3-fastjsonschema (2.21.1-1) ... 196s Selecting previously unselected package python3-platformdirs. 196s Preparing to unpack .../20-python3-platformdirs_4.3.6-1_all.deb ... 196s Unpacking python3-platformdirs (4.3.6-1) ... 196s Selecting previously unselected package python3-traitlets. 196s Preparing to unpack .../21-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 196s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 196s Selecting previously unselected package python3-jupyter-core. 196s Preparing to unpack .../22-python3-jupyter-core_5.7.2-5_all.deb ... 196s Unpacking python3-jupyter-core (5.7.2-5) ... 196s Selecting previously unselected package python3-nbformat. 196s Preparing to unpack .../23-python3-nbformat_5.9.1-1_all.deb ... 196s Unpacking python3-nbformat (5.9.1-1) ... 196s Selecting previously unselected package python3-tenacity. 196s Preparing to unpack .../24-python3-tenacity_8.5.0-0ubuntu1_all.deb ... 196s Unpacking python3-tenacity (8.5.0-0ubuntu1) ... 196s Selecting previously unselected package python3-plotly. 196s Preparing to unpack .../25-python3-plotly_5.20.0+dfsg-1_all.deb ... 196s Unpacking python3-plotly (5.20.0+dfsg-1) ... 197s Selecting previously unselected package python3-pysam. 197s Preparing to unpack .../26-python3-pysam_0.22.1+ds-2build1_arm64.deb ... 197s Unpacking python3-pysam (0.22.1+ds-2build1) ... 197s Selecting previously unselected package python3-scipy. 197s Preparing to unpack .../27-python3-scipy_1.14.1-3ubuntu1_arm64.deb ... 197s Unpacking python3-scipy (1.14.1-3ubuntu1) ... 198s Selecting previously unselected package python3-tqdm. 198s Preparing to unpack .../28-python3-tqdm_4.67.1-1_all.deb ... 198s Unpacking python3-tqdm (4.67.1-1) ... 198s Selecting previously unselected package python3-h5py. 198s Preparing to unpack .../29-python3-h5py_3.11.0-8ubuntu3_all.deb ... 198s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 198s Selecting previously unselected package pycoqc. 198s Preparing to unpack .../30-pycoqc_2.5.2+dfsg-3_all.deb ... 198s Unpacking pycoqc (2.5.2+dfsg-3) ... 198s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 198s Setting up python3-tenacity (8.5.0-0ubuntu1) ... 198s Setting up python3-tqdm (4.67.1-1) ... 199s Setting up libdeflate0:arm64 (1.22-1) ... 199s Setting up libaec0:arm64 (1.1.3-1) ... 199s Setting up python3-platformdirs (4.3.6-1) ... 199s Setting up python3-tz (2024.2-1) ... 199s Setting up python3-decorator (5.1.1-5) ... 199s Setting up libblas3:arm64 (3.12.0-4) ... 199s 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 199s Setting up liblzf1:arm64 (3.6-4) ... 199s Setting up libgfortran5:arm64 (14.2.0-12ubuntu1) ... 199s Setting up python3-fastjsonschema (2.21.1-1) ... 199s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 199s Setting up libhts3t64:arm64 (1.20+ds-2) ... 199s Setting up python3-dateutil (2.9.0-3) ... 200s Setting up python3-jupyter-core (5.7.2-5) ... 200s Setting up libsz2:arm64 (1.1.3-1) ... 200s Setting up liblapack3:arm64 (3.12.0-4) ... 200s 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 200s Setting up python3-pysam (0.22.1+ds-2build1) ... 200s Setting up python3-nbformat (5.9.1-1) ... 200s Setting up python3-plotly (5.20.0+dfsg-1) ... 206s Setting up python3-numpy (1:1.26.4+ds-12) ... 209s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-5ubuntu1) ... 209s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 209s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-5ubuntu1) ... 209s Setting up python3-scipy (1.14.1-3ubuntu1) ... 212s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5ubuntu1) ... 212s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 213s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 218s Setting up python3-h5py (3.11.0-8ubuntu3) ... 218s Setting up pycoqc (2.5.2+dfsg-3) ... 218s Processing triggers for libc-bin (2.40-4ubuntu1) ... 218s Processing triggers for man-db (2.13.0-1) ... 220s autopkgtest [07:13:19]: test run-unit-test: [----------------------- 221s Test 1 222s Checking arguments values 222s Check input data files 222s Parse data files 222s Merge data 222s Cleaning data 222s Loading plotting interface 223s PASS 223s 223s Test 2 223s Checking arguments values 223s Check input data files 223s Parse data files 223s Merge data 223s Cleaning data 223s Loading plotting interface 224s PASS 224s 224s Test 3 225s Checking arguments values 225s Check input data files 225s Parse data files 225s Merge data 225s Cleaning data 225s Loading plotting interface 226s PASS 226s 226s Test 4 226s Checking arguments values 226s Check input data files 226s Parse data files 226s Merge data 226s Cleaning data 227s Loading plotting interface 228s PASS 228s 228s Test 5 228s Checking arguments values 228s Check input data files 228s Parse data files 228s Merge data 228s Cleaning data 228s Loading plotting interface 229s PASS 229s 229s Test 6 230s PASS 230s 230s Test 7 231s Checking arguments values 231s Check input data files 231s Parse data files 231s Merge data 231s Cleaning data 231s Loading plotting interface 232s PASS 232s 232s Test 8 232s 0 reads [00:00, ? reads/s] 22 reads [00:00, 831.36 reads/s] 232s Total reads: 22 / Average speed: 524.65 reads/s 232s 233s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template 233s 3e81c32a-f2ee-4719-a88d-e0affe93d26f 40ebe55356ada6c830fa793745ef4c498d896c73 348 24 1137 8.124 filtered_out 233s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out 233s bcb20156-a5fe-4daa-aad9-b62c286e468d 40ebe55356ada6c830fa793745ef4c498d896c73 192 21 306 7.337 filtered_out 233s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out 233s 3f09025f-3d2c-4f84-9ea6-63dba736b649 40ebe55356ada6c830fa793745ef4c498d896c73 418 17 593 7.742 filtered_out 233s 1f83ee80-ac29-46be-b8bc-9dc9325f1fa7 40ebe55356ada6c830fa793745ef4c498d896c73 382 35 819 7.414 filtered_out 233s 9a1c5296-2ab1-4abd-8d50-e059754cf332 40ebe55356ada6c830fa793745ef4c498d896c73 319 33 1235 8.119 filtered_out 233s 6af04302-04c8-4d8d-8e87-aa69178b3f24 40ebe55356ada6c830fa793745ef4c498d896c73 36 26 832 8.234 filtered_out 233s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out 233s PASS 233s 233s Test 9 233s Check input data and options 233s Start processing fast5 files 233s 0 reads [00:00, ? reads/s] 22 reads [00:00, 1376.17 reads/s] 233s Overall counts valid files: 22 233s 233s fields found mean_qscore_template: 22 233s called_events: 22 233s duration: 22 233s strand_score: 22 233s 233s fields not found 233s Total reads: 22 / Average speed: 688.29 reads/s 233s 233s mean_qscore_template called_events duration strand_score 233s 8.23 2778 51387 -0.0007 233s 7.337 1972 29589 -0.0009 233s 9.407 2848 42730 -0.0003 233s 8.124 2978 44675 -0.0005 233s 8.119 3181 47720 -0.0004 233s 7.742 2142 32138 -0.0004 233s 7.414 3017 45267 -0.0002 233s 8.304 1547 23218 -0.0008 233s 8.234 1827 27409 -0.0011 233s PASS 233s 233s Test 10 234s Check input data and options 234s Start processing fast5 files 234s 0 reads [00:00, ? reads/s] 22 reads [00:00, 1327.92 reads/s] 234s Overall counts valid files: 22 234s 234s fields found read_id: 22 234s run_id: 22 234s channel: 22 234s start_time: 22 234s sequence_length_template: 22 234s mean_qscore_template: 22 234s calibration_strand_genome_template: 22 234s 234s fields not found barcode_arrangement: 22 234s 234s Total reads: 22 / Average speed: 561.6 reads/s 234s 234s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template path 234s 3e81c32a-f2ee-4719-a88d-e0affe93d26f 40ebe55356ada6c830fa793745ef4c498d896c73 348 24 1137 8.124 filtered_out /tmp/autopkgtest.TscvWl/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_348_strand.fast5 234s bcb20156-a5fe-4daa-aad9-b62c286e468d 40ebe55356ada6c830fa793745ef4c498d896c73 192 21 306 7.337 filtered_out /tmp/autopkgtest.TscvWl/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_192_strand.fast5 234s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out /tmp/autopkgtest.TscvWl/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_108_strand.fast5 234s 3f09025f-3d2c-4f84-9ea6-63dba736b649 40ebe55356ada6c830fa793745ef4c498d896c73 418 17 593 7.742 filtered_out /tmp/autopkgtest.TscvWl/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_418_strand.fast5 234s 9a1c5296-2ab1-4abd-8d50-e059754cf332 40ebe55356ada6c830fa793745ef4c498d896c73 319 33 1235 8.119 filtered_out /tmp/autopkgtest.TscvWl/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_319_strand.fast5 234s 1f83ee80-ac29-46be-b8bc-9dc9325f1fa7 40ebe55356ada6c830fa793745ef4c498d896c73 382 35 819 7.414 filtered_out /tmp/autopkgtest.TscvWl/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_382_strand.fast5 234s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out /tmp/autopkgtest.TscvWl/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_318_strand.fast5 234s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out /tmp/autopkgtest.TscvWl/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_191_strand.fast5 234s 6af04302-04c8-4d8d-8e87-aa69178b3f24 40ebe55356ada6c830fa793745ef4c498d896c73 36 26 832 8.234 filtered_out /tmp/autopkgtest.TscvWl/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_36_strand.fast5 234s PASS 234s 234s Test 11 235s Import data from sequencing summary file(s) and cleanup 235s Read files and import in a dataframe 235s Check input data files 235s Parse data files 235s Merge data 235s Cleanup missing barcodes values 236s Cleaning up low frequency barcodes 236s Split data per barcode 236s Processing data for Barcode barcode02 236s Processing data for Barcode barcode07 236s Processing data for Barcode barcode08 236s Processing data for Barcode barcode09 236s Processing data for Barcode barcode10 236s Processing data for Barcode barcode11 236s Processing data for Barcode barcode12 236s Processing data for Barcode unclassified 236s Barcode Counts 236s Counts Write 236s barcode02 2 False 236s barcode07 1 False 236s barcode08 30 False 236s barcode09 9945 True 236s barcode10 12644 True 236s barcode11 13594 True 236s barcode12 9813 True 236s unclassified 3971 False 236s PASS 236s 236s Test 12 237s General info 237s package_name: pycoQC 237s package_version: 2.5.2 237s timestamp: 2025-01-08 07:13:36.603151 237s 237s Runtime options 237s summary_file: ['Guppy-basecall-1D-DNA_sequencing_summary.txt'] 237s barcode_file: ['Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt'] 237s output_dir: results/ 237s output_unclassified: False 237s min_barcode_percent: 0.1 237s verbose: True 237s quiet: False 237s 237s Import data from sequencing summary file(s) and cleanup 237s Read files and import in a dataframe 237s Check input data files 237s Sequencing summary files found: Guppy-basecall-1D-DNA_sequencing_summary.txt 237s Barcode files found: Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt 237s Parse data files 237s Parse summary files 237s 3,999 reads found in initial file 237s Parse barcode files 237s Found valid Deepbinner barcode file 237s 3,775 reads with barcodes assigned 237s Merge data 237s Cleanup missing barcodes values 237s Cleaning up low frequency barcodes 237s Split data per barcode 237s Processing data for Barcode 1 237s Processing data for Barcode 2 237s Processing data for Barcode 3 237s Processing data for Barcode 4 237s Processing data for Barcode 5 237s Processing data for Barcode 6 237s Processing data for Barcode 7 237s Processing data for Barcode 8 237s Processing data for Barcode unclassified 237s Barcode Counts 237s Counts Write 237s 1 534 True 237s 2 206 True 237s 3 562 True 237s 4 579 True 237s 5 590 True 237s 6 655 True 237s 7 271 True 237s 8 378 True 237s unclassified 224 False 237s PASS 237s 237s Check if files really exist 237s PASS 237s 238s autopkgtest [07:13:37]: test run-unit-test: -----------------------] 238s autopkgtest [07:13:37]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 238s run-unit-test PASS 239s autopkgtest [07:13:38]: @@@@@@@@@@@@@@@@@@@@ summary 239s run-unit-test PASS 255s nova [W] Using flock in prodstack6-arm64 255s flock: timeout while waiting to get lock 255s Creating nova instance adt-plucky-arm64-pycoqc-20250108-070939-juju-7f2275-prod-proposed-migration-environment-20-0961f869-0bd4-407b-8d8b-5052f9be909e from image adt/ubuntu-plucky-arm64-server-20250107.img (UUID f1513a66-9218-43c0-bf67-63c4330d1399)... 255s nova [W] Timed out waiting for 63d08b61-4edb-4f5f-8b66-35a539a5009b to get deleted.