0s autopkgtest [17:31:26]: starting date and time: 2026-02-03 17:31:26+0000 0s autopkgtest [17:31:26]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [17:31:26]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.99vp07rf/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.46 lxd-armhf-10.145.243.46:autopkgtest/ubuntu/resolute/armhf 27s autopkgtest [17:31:53]: testbed dpkg architecture: armhf 29s autopkgtest [17:31:55]: testbed apt version: 3.1.14 33s autopkgtest [17:31:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 35s autopkgtest [17:32:01]: testbed release detected to be: None 43s autopkgtest [17:32:08]: updating testbed package index (apt update) 44s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 45s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 45s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 45s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 45s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 45s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [241 kB] 45s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1327 kB] 45s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [27.9 kB] 45s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [281 kB] 45s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1068 kB] 45s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [6336 B] 45s Get:12 http://ftpmaster.internal/ubuntu resolute/main Sources [1400 kB] 45s Get:13 http://ftpmaster.internal/ubuntu resolute/multiverse Sources [310 kB] 45s Get:14 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.3 MB] 48s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1373 kB] 49s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.1 MB] 49s Get:17 http://ftpmaster.internal/ubuntu resolute/multiverse armhf Packages [176 kB] 50s Fetched 43.2 MB in 5s (8295 kB/s) 51s Reading package lists... 57s autopkgtest [17:32:23]: upgrading testbed (apt dist-upgrade and autopurge) 58s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Calculating upgrade... 60s The following packages will be upgraded: 60s powermgmt-base python3-jinja2 systemd-hwe-hwdb 60s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s Need to get 120 kB of archives. 60s After this operation, 1024 B of additional disk space will be used. 60s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf systemd-hwe-hwdb all 259.0.1 [3152 B] 60s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf powermgmt-base all 1.38ubuntu2 [7878 B] 60s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-jinja2 all 3.1.6-1build1 [109 kB] 61s Fetched 120 kB in 0s (256 kB/s) 61s (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 ... 68394 files and directories currently installed.) 61s Preparing to unpack .../systemd-hwe-hwdb_259.0.1_all.deb ... 61s Unpacking systemd-hwe-hwdb (259.0.1) over (257.7.1) ... 61s Preparing to unpack .../powermgmt-base_1.38ubuntu2_all.deb ... 61s Unpacking powermgmt-base (1.38ubuntu2) over (1.38ubuntu1) ... 61s Preparing to unpack .../python3-jinja2_3.1.6-1build1_all.deb ... 61s Unpacking python3-jinja2 (3.1.6-1build1) over (3.1.6-1) ... 61s Setting up powermgmt-base (1.38ubuntu2) ... 61s Setting up python3-jinja2 (3.1.6-1build1) ... 61s Setting up systemd-hwe-hwdb (259.0.1) ... 62s Processing triggers for udev (259-1ubuntu3) ... 63s Processing triggers for man-db (2.13.1-1) ... 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s Solving dependencies... 67s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 69s autopkgtest [17:32:35]: rebooting testbed after setup commands that affected boot 113s autopkgtest [17:33:19]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 140s autopkgtest [17:33:46]: @@@@@@@@@@@@@@@@@@@@ apt-source pycoqc 159s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (dsc) [2027 B] 159s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (tar) [41.6 MB] 159s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pycoqc 2.5.2+dfsg-4 (diff) [6840 B] 159s gpgv: Signature made Sat Jan 18 02:09:23 2025 UTC 159s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 159s gpgv: issuer "tchet@debian.org" 159s gpgv: Can't check signature: No public key 159s dpkg-source: warning: cannot verify inline signature for ./pycoqc_2.5.2+dfsg-4.dsc: no acceptable signature found 161s autopkgtest [17:34:07]: testing package pycoqc version 2.5.2+dfsg-4 163s autopkgtest [17:34:09]: build not needed 167s autopkgtest [17:34:13]: test run-unit-test: preparing testbed 170s Reading package lists... 170s Building dependency tree... 170s Reading state information... 170s Solving dependencies... 171s The following NEW packages will be installed: 171s libblas3 libdeflate0 libgfortran5 libhdf5-310 libhdf5-hl-310 libhts3t64 171s libhtscodecs2 liblapack3 liblzf1 libqhull-r8.0 libsz2 pycoqc 171s python3-decorator python3-fastjsonschema python3-h5py python3-h5py-serial 171s python3-jupyter-core python3-nbformat python3-numpy python3-numpy-dev 171s python3-pandas python3-pandas-lib python3-platformdirs python3-plotly 171s python3-pysam python3-pytz python3-scipy python3-tenacity python3-tqdm 171s python3-traitlets 171s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 171s Need to get 47.0 MB of archives. 171s After this operation, 276 MB of additional disk space will be used. 171s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy-dev armhf 1:2.3.5+ds-3 [141 kB] 171s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 171s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-12ubuntu1 [334 kB] 171s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7ubuntu1 [2090 kB] 172s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy armhf 1:2.3.5+ds-3 [4729 kB] 172s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2 [38.7 kB] 172s Get:7 http://ftpmaster.internal/ubuntu resolute/universe armhf libsz2 armhf 1.1.5-1 [16.3 kB] 172s Get:8 http://ftpmaster.internal/ubuntu resolute/universe armhf libhdf5-310 armhf 1.14.6+repack-2 [1423 kB] 172s Get:9 http://ftpmaster.internal/ubuntu resolute/universe armhf libhdf5-hl-310 armhf 1.14.6+repack-2 [58.9 kB] 172s Get:10 http://ftpmaster.internal/ubuntu resolute/universe armhf libhtscodecs2 armhf 1.6.1-2build1 [67.0 kB] 172s Get:11 http://ftpmaster.internal/ubuntu resolute/universe armhf libhts3t64 armhf 1.22.1+ds2-1 [408 kB] 172s Get:12 http://ftpmaster.internal/ubuntu resolute/universe armhf liblzf1 armhf 3.6-4build1 [6592 B] 172s Get:13 http://ftpmaster.internal/ubuntu resolute/universe armhf libqhull-r8.0 armhf 2020.2-8 [175 kB] 172s Get:14 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-h5py-serial armhf 3.15.1-4 [1562 kB] 172s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-h5py all 3.15.1-4 [11.3 kB] 172s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pytz all 2025.2-5 [32.4 kB] 172s Get:17 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pandas-lib armhf 2.3.3+dfsg-3 [7022 kB] 173s Get:18 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pandas all 2.3.3+dfsg-3 [2948 kB] 173s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf python3-decorator all 5.2.1-2 [28.1 kB] 173s Get:20 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-fastjsonschema all 2.21.1-1 [20.4 kB] 173s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf python3-platformdirs all 4.5.1-1 [17.1 kB] 173s Get:22 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-traitlets all 5.14.3+really5.14.3-2 [71.7 kB] 173s Get:23 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-jupyter-core all 5.9.1-1 [28.9 kB] 173s Get:24 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-nbformat all 5.10.4-1 [39.2 kB] 173s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf python3-tenacity all 9.0.0-0ubuntu1 [17.0 kB] 173s Get:26 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-plotly all 5.20.0+dfsg-1.1 [2766 kB] 173s Get:27 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pysam armhf 0.23.3+ds-2 [4358 kB] 173s Get:28 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-scipy armhf 1.16.3-4 [18.3 MB] 174s Get:29 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-tqdm all 4.67.1-7 [93.3 kB] 174s Get:30 http://ftpmaster.internal/ubuntu resolute/universe armhf pycoqc all 2.5.2+dfsg-4 [36.4 kB] 174s Fetched 47.0 MB in 3s (15.2 MB/s) 174s Selecting previously unselected package python3-numpy-dev:armhf. 174s (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 ... 68395 files and directories currently installed.) 174s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_armhf.deb ... 174s Unpacking python3-numpy-dev:armhf (1:2.3.5+ds-3) ... 174s Selecting previously unselected package libblas3:armhf. 174s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_armhf.deb ... 174s Unpacking libblas3:armhf (3.12.1-7ubuntu1) ... 174s Selecting previously unselected package libgfortran5:armhf. 174s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_armhf.deb ... 174s Unpacking libgfortran5:armhf (15.2.0-12ubuntu1) ... 174s Selecting previously unselected package liblapack3:armhf. 174s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_armhf.deb ... 174s Unpacking liblapack3:armhf (3.12.1-7ubuntu1) ... 175s Selecting previously unselected package python3-numpy. 175s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_armhf.deb ... 175s Unpacking python3-numpy (1:2.3.5+ds-3) ... 175s Selecting previously unselected package libdeflate0:armhf. 175s Preparing to unpack .../05-libdeflate0_1.23-2_armhf.deb ... 175s Unpacking libdeflate0:armhf (1.23-2) ... 175s Selecting previously unselected package libsz2:armhf. 175s Preparing to unpack .../06-libsz2_1.1.5-1_armhf.deb ... 175s Unpacking libsz2:armhf (1.1.5-1) ... 175s Selecting previously unselected package libhdf5-310:armhf. 175s Preparing to unpack .../07-libhdf5-310_1.14.6+repack-2_armhf.deb ... 175s Unpacking libhdf5-310:armhf (1.14.6+repack-2) ... 175s Selecting previously unselected package libhdf5-hl-310:armhf. 175s Preparing to unpack .../08-libhdf5-hl-310_1.14.6+repack-2_armhf.deb ... 175s Unpacking libhdf5-hl-310:armhf (1.14.6+repack-2) ... 175s Selecting previously unselected package libhtscodecs2:armhf. 175s Preparing to unpack .../09-libhtscodecs2_1.6.1-2build1_armhf.deb ... 175s Unpacking libhtscodecs2:armhf (1.6.1-2build1) ... 175s Selecting previously unselected package libhts3t64:armhf. 175s Preparing to unpack .../10-libhts3t64_1.22.1+ds2-1_armhf.deb ... 175s Unpacking libhts3t64:armhf (1.22.1+ds2-1) ... 175s Selecting previously unselected package liblzf1:armhf. 175s Preparing to unpack .../11-liblzf1_3.6-4build1_armhf.deb ... 175s Unpacking liblzf1:armhf (3.6-4build1) ... 175s Selecting previously unselected package libqhull-r8.0:armhf. 175s Preparing to unpack .../12-libqhull-r8.0_2020.2-8_armhf.deb ... 175s Unpacking libqhull-r8.0:armhf (2020.2-8) ... 175s Selecting previously unselected package python3-h5py-serial. 175s Preparing to unpack .../13-python3-h5py-serial_3.15.1-4_armhf.deb ... 175s Unpacking python3-h5py-serial (3.15.1-4) ... 175s Selecting previously unselected package python3-h5py. 175s Preparing to unpack .../14-python3-h5py_3.15.1-4_all.deb ... 175s Unpacking python3-h5py (3.15.1-4) ... 175s Selecting previously unselected package python3-pytz. 175s Preparing to unpack .../15-python3-pytz_2025.2-5_all.deb ... 175s Unpacking python3-pytz (2025.2-5) ... 175s Selecting previously unselected package python3-pandas-lib:armhf. 175s Preparing to unpack .../16-python3-pandas-lib_2.3.3+dfsg-3_armhf.deb ... 175s Unpacking python3-pandas-lib:armhf (2.3.3+dfsg-3) ... 175s Selecting previously unselected package python3-pandas. 176s Preparing to unpack .../17-python3-pandas_2.3.3+dfsg-3_all.deb ... 176s Unpacking python3-pandas (2.3.3+dfsg-3) ... 176s Selecting previously unselected package python3-decorator. 176s Preparing to unpack .../18-python3-decorator_5.2.1-2_all.deb ... 176s Unpacking python3-decorator (5.2.1-2) ... 176s Selecting previously unselected package python3-fastjsonschema. 176s Preparing to unpack .../19-python3-fastjsonschema_2.21.1-1_all.deb ... 176s Unpacking python3-fastjsonschema (2.21.1-1) ... 176s Selecting previously unselected package python3-platformdirs. 176s Preparing to unpack .../20-python3-platformdirs_4.5.1-1_all.deb ... 176s Unpacking python3-platformdirs (4.5.1-1) ... 176s Selecting previously unselected package python3-traitlets. 176s Preparing to unpack .../21-python3-traitlets_5.14.3+really5.14.3-2_all.deb ... 176s Unpacking python3-traitlets (5.14.3+really5.14.3-2) ... 176s Selecting previously unselected package python3-jupyter-core. 176s Preparing to unpack .../22-python3-jupyter-core_5.9.1-1_all.deb ... 176s Unpacking python3-jupyter-core (5.9.1-1) ... 176s Selecting previously unselected package python3-nbformat. 176s Preparing to unpack .../23-python3-nbformat_5.10.4-1_all.deb ... 176s Unpacking python3-nbformat (5.10.4-1) ... 176s Selecting previously unselected package python3-tenacity. 176s Preparing to unpack .../24-python3-tenacity_9.0.0-0ubuntu1_all.deb ... 176s Unpacking python3-tenacity (9.0.0-0ubuntu1) ... 176s Selecting previously unselected package python3-plotly. 176s Preparing to unpack .../25-python3-plotly_5.20.0+dfsg-1.1_all.deb ... 176s Unpacking python3-plotly (5.20.0+dfsg-1.1) ... 178s Selecting previously unselected package python3-pysam. 178s Preparing to unpack .../26-python3-pysam_0.23.3+ds-2_armhf.deb ... 178s Unpacking python3-pysam (0.23.3+ds-2) ... 178s Selecting previously unselected package python3-scipy. 178s Preparing to unpack .../27-python3-scipy_1.16.3-4_armhf.deb ... 178s Unpacking python3-scipy (1.16.3-4) ... 179s Selecting previously unselected package python3-tqdm. 179s Preparing to unpack .../28-python3-tqdm_4.67.1-7_all.deb ... 179s Unpacking python3-tqdm (4.67.1-7) ... 179s Selecting previously unselected package pycoqc. 179s Preparing to unpack .../29-pycoqc_2.5.2+dfsg-4_all.deb ... 179s Unpacking pycoqc (2.5.2+dfsg-4) ... 179s Setting up libhtscodecs2:armhf (1.6.1-2build1) ... 179s Setting up python3-tenacity (9.0.0-0ubuntu1) ... 179s Setting up python3-tqdm (4.67.1-7) ... 180s Setting up libdeflate0:armhf (1.23-2) ... 180s Setting up libqhull-r8.0:armhf (2020.2-8) ... 180s Setting up python3-pytz (2025.2-5) ... 180s Setting up python3-platformdirs (4.5.1-1) ... 180s Setting up python3-decorator (5.2.1-2) ... 180s Setting up libblas3:armhf (3.12.1-7ubuntu1) ... 180s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 180s Setting up liblzf1:armhf (3.6-4build1) ... 180s Setting up python3-numpy-dev:armhf (1:2.3.5+ds-3) ... 180s Setting up libgfortran5:armhf (15.2.0-12ubuntu1) ... 180s Setting up python3-fastjsonschema (2.21.1-1) ... 180s Setting up python3-traitlets (5.14.3+really5.14.3-2) ... 181s Setting up libhts3t64:armhf (1.22.1+ds2-1) ... 181s Setting up python3-jupyter-core (5.9.1-1) ... 181s Setting up libsz2:armhf (1.1.5-1) ... 181s Setting up liblapack3:armhf (3.12.1-7ubuntu1) ... 181s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 181s Setting up python3-pysam (0.23.3+ds-2) ... 181s Setting up python3-nbformat (5.10.4-1) ... 181s Setting up python3-plotly (5.20.0+dfsg-1.1) ... 188s Setting up python3-numpy (1:2.3.5+ds-3) ... 190s Setting up libhdf5-310:armhf (1.14.6+repack-2) ... 190s Setting up libhdf5-hl-310:armhf (1.14.6+repack-2) ... 190s Setting up python3-scipy (1.16.3-4) ... 195s Setting up python3-pandas-lib:armhf (2.3.3+dfsg-3) ... 195s Setting up python3-h5py-serial (3.15.1-4) ... 195s Setting up python3-pandas (2.3.3+dfsg-3) ... 200s Setting up python3-h5py (3.15.1-4) ... 201s Setting up pycoqc (2.5.2+dfsg-4) ... 201s Processing triggers for libc-bin (2.42-2ubuntu4) ... 201s Processing triggers for man-db (2.13.1-1) ... 210s autopkgtest [17:34:56]: test run-unit-test: [----------------------- 213s Test 1 214s Checking arguments values 214s Check input data files 214s Parse data files 214s Merge data 214s Cleaning data 214s Loading plotting interface 215s PASS 215s 215s Test 2 215s Checking arguments values 215s Check input data files 215s Parse data files 215s Merge data 215s Cleaning data 215s Loading plotting interface 216s PASS 216s 216s Test 3 217s Checking arguments values 217s Check input data files 217s Parse data files 217s Merge data 217s Cleaning data 217s Loading plotting interface 218s PASS 218s 218s Test 4 219s Checking arguments values 219s Check input data files 219s Parse data files 219s Merge data 219s Cleaning data 219s Loading plotting interface 220s PASS 220s 220s Test 5 221s Checking arguments values 221s Check input data files 221s Parse data files 221s Merge data 221s Cleaning data 221s Loading plotting interface 222s PASS 222s 222s Test 6 223s PASS 223s 223s Test 7 224s Checking arguments values 224s Check input data files 224s Parse data files 224s Merge data 224s Cleaning data 224s Loading plotting interface 225s PASS 225s 225s Test 8 226s 0 reads [00:00, ? reads/s] 22 reads [00:00, 352.12 reads/s] 226s Total reads: 22 / Average speed: 275.66 reads/s 226s 226s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template 226s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out 226s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out 226s c38cbad9-d91e-4208-9317-832f4e2cc289 40ebe55356ada6c830fa793745ef4c498d896c73 113 30 824 8.693 filtered_out 226s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out 226s 5b7fadd0-c646-4c7b-9800-66ee658a5ca8 40ebe55356ada6c830fa793745ef4c498d896c73 150 37 468 7.608 filtered_out 226s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out 226s bcb20156-a5fe-4daa-aad9-b62c286e468d 40ebe55356ada6c830fa793745ef4c498d896c73 192 21 306 7.337 filtered_out 226s ed05c5e6-7aab-4970-a431-3411047764a6 40ebe55356ada6c830fa793745ef4c498d896c73 224 34 880 8.891 filtered_out 226s 2c32553e-62c6-4c7a-bf05-249771364f04 40ebe55356ada6c830fa793745ef4c498d896c73 237 11 1151 8.544 filtered_out 226s PASS 226s 226s Test 9 227s Check input data and options 227s Start processing fast5 files 227s 0 reads [00:00, ? reads/s] 22 reads [00:00, 2083.89 reads/s] 227s Overall counts valid files: 22 227s 227s fields found mean_qscore_template: 22 227s called_events: 22 227s duration: 22 227s strand_score: 22 227s 227s fields not found 227s Total reads: 22 / Average speed: 926.94 reads/s 227s 228s mean_qscore_template called_events duration strand_score 228s 8.56 5838 87570 -0.0003 228s 8.693 2383 35752 -0.0005 228s 7.805 1438 21583 -0.0006 228s 9.407 2848 42730 -0.0003 228s 7.608 1615 24233 -0.0007 228s 8.23 2778 51387 -0.0007 228s 7.337 1972 29589 -0.0009 228s 8.891 2774 41612 -0.0006 228s 8.544 3740 56107 -0.0003 228s PASS 228s 228s Test 10 228s Check input data and options 228s Start processing fast5 files 228s 0 reads [00:00, ? reads/s] 22 reads [00:00, 1132.43 reads/s] 228s Overall counts valid files: 22 228s 228s fields found read_id: 22 228s run_id: 22 228s channel: 22 228s start_time: 22 228s sequence_length_template: 22 228s mean_qscore_template: 22 228s calibration_strand_genome_template: 22 228s 228s fields not found barcode_arrangement: 22 228s 228s Total reads: 22 / Average speed: 673.56 reads/s 228s 228s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template path 228s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out /tmp/autopkgtest.J7rOYw/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_103_strand.fast5 228s c38cbad9-d91e-4208-9317-832f4e2cc289 40ebe55356ada6c830fa793745ef4c498d896c73 113 30 824 8.693 filtered_out /tmp/autopkgtest.J7rOYw/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_113_strand.fast5 228s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out /tmp/autopkgtest.J7rOYw/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_108_strand.fast5 228s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out /tmp/autopkgtest.J7rOYw/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_121_strand.fast5 228s 5b7fadd0-c646-4c7b-9800-66ee658a5ca8 40ebe55356ada6c830fa793745ef4c498d896c73 150 37 468 7.608 filtered_out /tmp/autopkgtest.J7rOYw/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_150_strand.fast5 228s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out /tmp/autopkgtest.J7rOYw/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_191_strand.fast5 228s ed05c5e6-7aab-4970-a431-3411047764a6 40ebe55356ada6c830fa793745ef4c498d896c73 224 34 880 8.891 filtered_out /tmp/autopkgtest.J7rOYw/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_224_strand.fast5 228s bcb20156-a5fe-4daa-aad9-b62c286e468d 40ebe55356ada6c830fa793745ef4c498d896c73 192 21 306 7.337 filtered_out /tmp/autopkgtest.J7rOYw/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_192_strand.fast5 228s 2c32553e-62c6-4c7a-bf05-249771364f04 40ebe55356ada6c830fa793745ef4c498d896c73 237 11 1151 8.544 filtered_out /tmp/autopkgtest.J7rOYw/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_237_strand.fast5 228s PASS 228s 228s Test 11 229s Import data from sequencing summary file(s) and cleanup 229s Read files and import in a dataframe 229s Check input data files 229s Parse data files 230s Merge data 230s Cleanup missing barcodes values 230s Cleaning up low frequency barcodes 230s Split data per barcode 230s Processing data for Barcode barcode02 230s Processing data for Barcode barcode07 230s Processing data for Barcode barcode08 230s Processing data for Barcode barcode09 230s Processing data for Barcode barcode10 230s Processing data for Barcode barcode11 231s Processing data for Barcode barcode12 231s Processing data for Barcode unclassified 231s Barcode Counts 231s Counts Write 231s barcode02 2 False 231s barcode07 1 False 231s barcode08 30 False 231s barcode09 9945 True 231s barcode10 12644 True 231s barcode11 13594 True 231s barcode12 9813 True 231s unclassified 3971 False 231s PASS 231s 231s Test 12 232s General info 232s package_name: pycoQC 232s package_version: 2.5.2 232s timestamp: 2026-02-03 17:35:18.227206 232s 232s Runtime options 232s summary_file: ['Guppy-basecall-1D-DNA_sequencing_summary.txt'] 232s barcode_file: ['Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt'] 232s output_dir: results/ 232s output_unclassified: False 232s min_barcode_percent: 0.1 232s verbose: True 232s quiet: False 232s 232s Import data from sequencing summary file(s) and cleanup 232s Read files and import in a dataframe 232s Check input data files 232s Sequencing summary files found: Guppy-basecall-1D-DNA_sequencing_summary.txt 232s Barcode files found: Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt 232s Parse data files 232s Parse summary files 232s 3,999 reads found in initial file 232s Parse barcode files 232s Found valid Deepbinner barcode file 232s 3,775 reads with barcodes assigned 232s Merge data 232s Cleanup missing barcodes values 232s Cleaning up low frequency barcodes 232s Split data per barcode 232s Processing data for Barcode 1 232s Processing data for Barcode 2 232s Processing data for Barcode 3 232s Processing data for Barcode 4 232s Processing data for Barcode 5 232s Processing data for Barcode 6 232s Processing data for Barcode 7 232s Processing data for Barcode 8 232s Processing data for Barcode unclassified 232s Barcode Counts 232s Counts Write 232s 1 534 True 232s 2 206 True 232s 3 562 True 232s 4 579 True 232s 5 590 True 232s 6 655 True 232s 7 271 True 232s 8 378 True 232s unclassified 224 False 232s PASS 232s 232s Check if files really exist 232s PASS 232s 232s autopkgtest [17:35:18]: test run-unit-test: -----------------------] 237s autopkgtest [17:35:23]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 237s run-unit-test PASS 241s autopkgtest [17:35:27]: @@@@@@@@@@@@@@@@@@@@ summary 241s run-unit-test PASS