0s autopkgtest [05:37:56]: starting date and time: 2026-01-30 05:37:56+0000 0s autopkgtest [05:37:56]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [05:37:56]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.l7gz8lad/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:ruamel.yaml --apt-upgrade toil --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=ruamel.yaml/0.18.10+ds-1build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu4-ram16-disk100-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-arm64-15.secgroup --name adt-resolute-arm64-toil-20260130-053755-juju-7f2275-prod-proposed-migration-environment-20-a369c776-3394-4297-a2ac-3fb10a5e9ed2 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-toil-20260130-053755-juju-7f2275-prod-proposed-migration-environment-20-a369c776-3394-4297-a2ac-3fb10a5e9ed2 from image adt/ubuntu-resolute-arm64-server-20260130.img (UUID d80a3628-95a8-4c17-a25a-26b02882b363)... 71s autopkgtest [05:39:07]: testbed dpkg architecture: arm64 71s autopkgtest [05:39:07]: testbed apt version: 3.1.14 71s autopkgtest [05:39:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 72s autopkgtest [05:39:08]: testbed release detected to be: None 72s autopkgtest [05:39:08]: updating testbed package index (apt update) 73s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 73s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 73s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 73s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 73s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1600 kB] 73s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [33.0 kB] 73s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [103 kB] 73s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 73s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [120 kB] 73s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [4364 B] 73s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [12.3 kB] 74s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [328 B] 74s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1166 kB] 74s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [21.9 kB] 74s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [25.4 kB] 74s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [720 B] 76s Fetched 3215 kB in 1s (2594 kB/s) 77s Reading package lists... 78s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 78s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 78s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 78s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 79s Reading package lists... 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s Calculating upgrade... 80s The following packages will be upgraded: 80s bzip2 inetutils-telnet libbz2-1.0 libsqlite3-0 telnet 80s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s Need to get 888 kB of archives. 80s After this operation, 2048 B of additional disk space will be used. 80s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 bzip2 arm64 1.0.8-6build2 [34.0 kB] 80s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libbz2-1.0 arm64 1.0.8-6build2 [34.9 kB] 80s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libsqlite3-0 arm64 3.46.1-9 [711 kB] 80s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 inetutils-telnet arm64 2:2.7-2ubuntu1 [104 kB] 80s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 telnet all 0.17+2.7-2ubuntu1 [3636 B] 80s dpkg-preconfigure: unable to re-open stdin: No such file or directory 81s Fetched 888 kB in 0s (3210 kB/s) 81s (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 ... 135255 files and directories currently installed.) 81s Preparing to unpack .../bzip2_1.0.8-6build2_arm64.deb ... 81s Unpacking bzip2 (1.0.8-6build2) over (1.0.8-6build1) ... 81s Preparing to unpack .../libbz2-1.0_1.0.8-6build2_arm64.deb ... 81s Unpacking libbz2-1.0:arm64 (1.0.8-6build2) over (1.0.8-6build1) ... 81s Setting up libbz2-1.0:arm64 (1.0.8-6build2) ... 81s (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 ... 135255 files and directories currently installed.) 81s Preparing to unpack .../libsqlite3-0_3.46.1-9_arm64.deb ... 81s Unpacking libsqlite3-0:arm64 (3.46.1-9) over (3.46.1-8) ... 81s Preparing to unpack .../inetutils-telnet_2%3a2.7-2ubuntu1_arm64.deb ... 81s Unpacking inetutils-telnet (2:2.7-2ubuntu1) over (2:2.6-4ubuntu1) ... 81s Preparing to unpack .../telnet_0.17+2.7-2ubuntu1_all.deb ... 81s Unpacking telnet (0.17+2.7-2ubuntu1) over (0.17+2.6-4ubuntu1) ... 81s Setting up libsqlite3-0:arm64 (3.46.1-9) ... 81s Setting up inetutils-telnet (2:2.7-2ubuntu1) ... 81s Setting up bzip2 (1.0.8-6build2) ... 82s Setting up telnet (0.17+2.7-2ubuntu1) ... 82s Processing triggers for man-db (2.13.1-1) ... 82s Processing triggers for libc-bin (2.42-2ubuntu4) ... 82s autopkgtest [05:39:18]: upgrading testbed (apt dist-upgrade and autopurge) 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s Calculating upgrade... 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Solving dependencies... 85s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s autopkgtest [05:39:23]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:41:39 UTC 2026 87s autopkgtest [05:39:23]: @@@@@@@@@@@@@@@@@@@@ apt-source toil 90s Get:1 http://ftpmaster.internal/ubuntu resolute/universe toil 9.1.0-1 (dsc) [2872 B] 90s Get:2 http://ftpmaster.internal/ubuntu resolute/universe toil 9.1.0-1 (tar) [7876 kB] 90s Get:3 http://ftpmaster.internal/ubuntu resolute/universe toil 9.1.0-1 (diff) [17.1 kB] 90s gpgv: Signature made Fri Oct 17 09:42:43 2025 UTC 90s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 90s gpgv: issuer "crusoe@debian.org" 90s gpgv: Can't check signature: No public key 90s dpkg-source: warning: cannot verify inline signature for ./toil_9.1.0-1.dsc: no acceptable signature found 90s autopkgtest [05:39:26]: testing package toil version 9.1.0-1 90s autopkgtest [05:39:26]: build not needed 93s autopkgtest [05:39:29]: test smoke-test: preparing testbed 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 93s Solving dependencies... 94s The following NEW packages will be installed: 94s cwl-upgrader cwltool fontconfig fontconfig-config fonts-dejavu-core 94s fonts-dejavu-mono fonts-glyphicons-halflings graphviz libaom3 libcairo2 94s libcdt6 libcgraph8 libdatrie1 libde265-0 libdeflate0 libfontconfig1 libgd3 94s libgomp1 libgraphite2-3 libgvc7 libgvplugin-gd8 libgvplugin-pango8 libgvpr2 94s libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265 libheif1 94s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap liblerc4 94s libltdl7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 94s libpixman-1-0 libsharpyuv0 libthai-data libthai0 libtiff6 libwebp7 94s libxcb-render0 libxcb-shm0 libxdot4 libxpm4 libxrender1 libxslt1.1 94s python3-arcp python3-argcomplete python3-blessed python3-cachecontrol 94s python3-coloredlogs python3-configargparse python3-cwl-utils python3-dill 94s python3-docker python3-enlighten python3-filelock python3-humanfriendly 94s python3-lxml python3-mistune python3-msgpack python3-mypy-extensions 94s python3-networkx python3-prefixed python3-prompt-toolkit python3-prov 94s python3-psutil python3-pubsub python3-pydot python3-rdflib 94s python3-rich-argparse python3-ruamel.yaml python3-ruamel.yaml.clib 94s python3-schema-salad python3-spython python3-wcwidth toil 94s 0 upgraded, 81 newly installed, 0 to remove and 0 not upgraded. 94s Need to get 28.0 MB of archives. 94s After this operation, 168 MB of additional disk space will be used. 94s Get:1 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-ruamel.yaml.clib arm64 0.2.15+ds-1 [178 kB] 94s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-ruamel.yaml all 0.18.10+ds-1build1 [127 kB] 94s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-msgpack arm64 1.1.2-1 [102 kB] 94s Get:4 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-cachecontrol all 0.14.3-1 [18.7 kB] 94s Get:5 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mistune all 3.1.4-1 [35.0 kB] 94s Get:6 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mypy-extensions all 1.1.0-1 [6716 B] 94s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-rdflib all 7.4.0-1 [431 kB] 94s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-filelock all 3.20.3-1 [13.5 kB] 94s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 94s Get:10 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 94s Get:11 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-schema-salad arm64 8.9.20251102115403-1 [1742 kB] 94s Get:12 http://ftpmaster.internal/ubuntu resolute/universe arm64 cwl-upgrader all 1.2.14-1 [16.6 kB] 94s Get:13 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-argcomplete all 3.6.3-1 [36.1 kB] 94s Get:14 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-humanfriendly all 10.0-6build1 [70.9 kB] 94s Get:15 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-coloredlogs all 15.0.1-1build1 [38.4 kB] 94s Get:16 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-cwl-utils all 0.40-1 [140 kB] 94s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libxslt1.1 arm64 1.1.43-0.3 [172 kB] 94s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-lxml arm64 6.0.2-1 [2155 kB] 94s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-networkx all 3.2.1-4ubuntu2 [11.8 MB] 94s Get:20 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcdt6 arm64 14.1.1-2ubuntu2 [19.0 kB] 94s Get:21 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcgraph8 arm64 14.1.1-2ubuntu2 [53.6 kB] 95s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libltdl7 arm64 2.5.4-9 [43.3 kB] 95s Get:23 http://ftpmaster.internal/ubuntu resolute/universe arm64 libpathplan4 arm64 14.1.1-2ubuntu2 [24.7 kB] 95s Get:24 http://ftpmaster.internal/ubuntu resolute/universe arm64 libxdot4 arm64 14.1.1-2ubuntu2 [23.0 kB] 95s Get:25 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgvc7 arm64 14.1.1-2ubuntu2 [371 kB] 95s Get:26 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgvpr2 arm64 14.1.1-2ubuntu2 [122 kB] 95s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 95s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8build1 [834 kB] 95s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.17.1-3ubuntu1 [38.5 kB] 95s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.17.1-3ubuntu1 [144 kB] 95s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 95s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2ubuntu1 [16.4 kB] 95s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2ubuntu1 [5938 B] 95s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 95s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-3 [556 kB] 95s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1build1 [16.7 kB] 95s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libaom3 arm64 3.13.1-2 [1773 kB] 95s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libheif-plugin-aomdec arm64 1.21.2-1 [13.9 kB] 95s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libde265-0 arm64 1.0.16-1build1 [148 kB] 95s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libheif-plugin-libde265 arm64 1.21.2-1 [9696 B] 95s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libheif1 arm64 1.21.2-1 [502 kB] 95s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-12ubuntu1 [147 kB] 95s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 95s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB] 95s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 95s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 95s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu3 [29.2 kB] 95s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu2 [174 kB] 95s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1build1 [205 kB] 95s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 95s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 libxpm4 arm64 1:3.5.17-1build3 [35.5 kB] 95s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 libgd3 arm64 2.3.3-13ubuntu1 [124 kB] 95s Get:53 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgvplugin-gd8 arm64 14.1.1-2ubuntu2 [24.8 kB] 95s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig arm64 2.17.1-3ubuntu1 [181 kB] 95s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-11ubuntu1 [72.1 kB] 95s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.3.1-1 [510 kB] 95s Get:57 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai-data all 0.1.30-1 [155 kB] 95s Get:58 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.14-1 [19.6 kB] 95s Get:59 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai0 arm64 0.1.30-1 [18.3 kB] 95s Get:60 http://ftpmaster.internal/ubuntu resolute/main arm64 libpango-1.0-0 arm64 1.57.0-1 [238 kB] 95s Get:61 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoft2-1.0-0 arm64 1.57.0-1 [51.5 kB] 95s Get:62 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangocairo-1.0-0 arm64 1.57.0-1 [27.9 kB] 95s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgvplugin-pango8 arm64 14.1.1-2ubuntu2 [23.0 kB] 95s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 graphviz arm64 14.1.1-2ubuntu2 [58.6 kB] 95s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pydot all 4.0.1-1 [35.8 kB] 95s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-prov all 2.1.1-1 [101 kB] 95s Get:67 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-psutil arm64 7.1.0-1ubuntu1 [191 kB] 95s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-rich-argparse all 1.6.0-2 [17.2 kB] 95s Get:69 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-spython all 0.3.13-2build1 [56.4 kB] 95s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-arcp all 0.2.1-7build1 [14.1 kB] 95s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 cwltool all 3.1.20251031082601-1 [533 kB] 95s Get:72 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-wcwidth all 0.2.14+dfsg1-1build1 [26.5 kB] 95s Get:73 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-blessed all 1.21.0-1 [50.4 kB] 95s Get:74 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-configargparse all 1.7-2 [31.7 kB] 95s Get:75 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-dill all 0.4.0-1 [84.8 kB] 95s Get:76 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-docker all 7.1.0-2ubuntu1 [91.0 kB] 95s Get:77 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-prefixed all 0.7.0-1build1 [8352 B] 95s Get:78 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-enlighten arm64 1.11.2-1build1 [42.4 kB] 95s Get:79 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-prompt-toolkit all 3.0.52-2 [258 kB] 95s Get:80 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pubsub all 4.0.3-7build1 [45.0 kB] 95s Get:81 http://ftpmaster.internal/ubuntu resolute/universe arm64 toil all 9.1.0-1 [1104 kB] 96s Fetched 28.0 MB in 2s (17.4 MB/s) 96s Selecting previously unselected package python3-ruamel.yaml.clib. 96s (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 ... 135255 files and directories currently installed.) 96s Preparing to unpack .../00-python3-ruamel.yaml.clib_0.2.15+ds-1_arm64.deb ... 96s Unpacking python3-ruamel.yaml.clib (0.2.15+ds-1) ... 96s Selecting previously unselected package python3-ruamel.yaml. 96s Preparing to unpack .../01-python3-ruamel.yaml_0.18.10+ds-1build1_all.deb ... 96s Unpacking python3-ruamel.yaml (0.18.10+ds-1build1) ... 96s Selecting previously unselected package python3-msgpack. 96s Preparing to unpack .../02-python3-msgpack_1.1.2-1_arm64.deb ... 96s Unpacking python3-msgpack (1.1.2-1) ... 96s Selecting previously unselected package python3-cachecontrol. 96s Preparing to unpack .../03-python3-cachecontrol_0.14.3-1_all.deb ... 96s Unpacking python3-cachecontrol (0.14.3-1) ... 96s Selecting previously unselected package python3-mistune. 96s Preparing to unpack .../04-python3-mistune_3.1.4-1_all.deb ... 96s Unpacking python3-mistune (3.1.4-1) ... 96s Selecting previously unselected package python3-mypy-extensions. 96s Preparing to unpack .../05-python3-mypy-extensions_1.1.0-1_all.deb ... 96s Unpacking python3-mypy-extensions (1.1.0-1) ... 96s Selecting previously unselected package python3-rdflib. 96s Preparing to unpack .../06-python3-rdflib_7.4.0-1_all.deb ... 96s Unpacking python3-rdflib (7.4.0-1) ... 96s Selecting previously unselected package python3-filelock. 96s Preparing to unpack .../07-python3-filelock_3.20.3-1_all.deb ... 96s Unpacking python3-filelock (3.20.3-1) ... 96s Selecting previously unselected package fonts-glyphicons-halflings. 96s Preparing to unpack .../08-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 96s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 96s Selecting previously unselected package libjs-bootstrap. 96s Preparing to unpack .../09-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 96s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 96s Selecting previously unselected package python3-schema-salad. 96s Preparing to unpack .../10-python3-schema-salad_8.9.20251102115403-1_arm64.deb ... 96s Unpacking python3-schema-salad (8.9.20251102115403-1) ... 96s Selecting previously unselected package cwl-upgrader. 96s Preparing to unpack .../11-cwl-upgrader_1.2.14-1_all.deb ... 96s Unpacking cwl-upgrader (1.2.14-1) ... 96s Selecting previously unselected package python3-argcomplete. 96s Preparing to unpack .../12-python3-argcomplete_3.6.3-1_all.deb ... 96s Unpacking python3-argcomplete (3.6.3-1) ... 96s Selecting previously unselected package python3-humanfriendly. 96s Preparing to unpack .../13-python3-humanfriendly_10.0-6build1_all.deb ... 96s Unpacking python3-humanfriendly (10.0-6build1) ... 96s Selecting previously unselected package python3-coloredlogs. 96s Preparing to unpack .../14-python3-coloredlogs_15.0.1-1build1_all.deb ... 96s Unpacking python3-coloredlogs (15.0.1-1build1) ... 96s Selecting previously unselected package python3-cwl-utils. 96s Preparing to unpack .../15-python3-cwl-utils_0.40-1_all.deb ... 96s Unpacking python3-cwl-utils (0.40-1) ... 96s Selecting previously unselected package libxslt1.1:arm64. 96s Preparing to unpack .../16-libxslt1.1_1.1.43-0.3_arm64.deb ... 96s Unpacking libxslt1.1:arm64 (1.1.43-0.3) ... 96s Selecting previously unselected package python3-lxml:arm64. 96s Preparing to unpack .../17-python3-lxml_6.0.2-1_arm64.deb ... 96s Unpacking python3-lxml:arm64 (6.0.2-1) ... 97s Selecting previously unselected package python3-networkx. 97s Preparing to unpack .../18-python3-networkx_3.2.1-4ubuntu2_all.deb ... 97s Unpacking python3-networkx (3.2.1-4ubuntu2) ... 97s Selecting previously unselected package libcdt6:arm64. 97s Preparing to unpack .../19-libcdt6_14.1.1-2ubuntu2_arm64.deb ... 97s Unpacking libcdt6:arm64 (14.1.1-2ubuntu2) ... 97s Selecting previously unselected package libcgraph8:arm64. 97s Preparing to unpack .../20-libcgraph8_14.1.1-2ubuntu2_arm64.deb ... 97s Unpacking libcgraph8:arm64 (14.1.1-2ubuntu2) ... 97s Selecting previously unselected package libltdl7:arm64. 97s Preparing to unpack .../21-libltdl7_2.5.4-9_arm64.deb ... 97s Unpacking libltdl7:arm64 (2.5.4-9) ... 97s Selecting previously unselected package libpathplan4:arm64. 97s Preparing to unpack .../22-libpathplan4_14.1.1-2ubuntu2_arm64.deb ... 97s Unpacking libpathplan4:arm64 (14.1.1-2ubuntu2) ... 97s Selecting previously unselected package libxdot4:arm64. 97s Preparing to unpack .../23-libxdot4_14.1.1-2ubuntu2_arm64.deb ... 97s Unpacking libxdot4:arm64 (14.1.1-2ubuntu2) ... 97s Selecting previously unselected package libgvc7:arm64. 97s Preparing to unpack .../24-libgvc7_14.1.1-2ubuntu2_arm64.deb ... 97s Unpacking libgvc7:arm64 (14.1.1-2ubuntu2) ... 97s Selecting previously unselected package libgvpr2:arm64. 97s Preparing to unpack .../25-libgvpr2_14.1.1-2ubuntu2_arm64.deb ... 97s Unpacking libgvpr2:arm64 (14.1.1-2ubuntu2) ... 97s Selecting previously unselected package fonts-dejavu-mono. 97s Preparing to unpack .../26-fonts-dejavu-mono_2.37-8build1_all.deb ... 97s Unpacking fonts-dejavu-mono (2.37-8build1) ... 97s Selecting previously unselected package fonts-dejavu-core. 97s Preparing to unpack .../27-fonts-dejavu-core_2.37-8build1_all.deb ... 97s Unpacking fonts-dejavu-core (2.37-8build1) ... 97s Selecting previously unselected package fontconfig-config. 98s Preparing to unpack .../28-fontconfig-config_2.17.1-3ubuntu1_arm64.deb ... 98s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 98s Selecting previously unselected package libfontconfig1:arm64. 98s Preparing to unpack .../29-libfontconfig1_2.17.1-3ubuntu1_arm64.deb ... 98s Unpacking libfontconfig1:arm64 (2.17.1-3ubuntu1) ... 98s Selecting previously unselected package libpixman-1-0:arm64. 98s Preparing to unpack .../30-libpixman-1-0_0.46.4-1_arm64.deb ... 98s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 98s Selecting previously unselected package libxcb-render0:arm64. 98s Preparing to unpack .../31-libxcb-render0_1.17.0-2ubuntu1_arm64.deb ... 98s Unpacking libxcb-render0:arm64 (1.17.0-2ubuntu1) ... 98s Selecting previously unselected package libxcb-shm0:arm64. 98s Preparing to unpack .../32-libxcb-shm0_1.17.0-2ubuntu1_arm64.deb ... 98s Unpacking libxcb-shm0:arm64 (1.17.0-2ubuntu1) ... 98s Selecting previously unselected package libxrender1:arm64. 98s Preparing to unpack .../33-libxrender1_1%3a0.9.12-1_arm64.deb ... 98s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 98s Selecting previously unselected package libcairo2:arm64. 98s Preparing to unpack .../34-libcairo2_1.18.4-3_arm64.deb ... 98s Unpacking libcairo2:arm64 (1.18.4-3) ... 98s Selecting previously unselected package libsharpyuv0:arm64. 98s Preparing to unpack .../35-libsharpyuv0_1.5.0-0.1build1_arm64.deb ... 98s Unpacking libsharpyuv0:arm64 (1.5.0-0.1build1) ... 98s Selecting previously unselected package libaom3:arm64. 98s Preparing to unpack .../36-libaom3_3.13.1-2_arm64.deb ... 98s Unpacking libaom3:arm64 (3.13.1-2) ... 98s Selecting previously unselected package libheif-plugin-aomdec:arm64. 98s Preparing to unpack .../37-libheif-plugin-aomdec_1.21.2-1_arm64.deb ... 98s Unpacking libheif-plugin-aomdec:arm64 (1.21.2-1) ... 98s Selecting previously unselected package libde265-0:arm64. 98s Preparing to unpack .../38-libde265-0_1.0.16-1build1_arm64.deb ... 98s Unpacking libde265-0:arm64 (1.0.16-1build1) ... 98s Selecting previously unselected package libheif-plugin-libde265:arm64. 98s Preparing to unpack .../39-libheif-plugin-libde265_1.21.2-1_arm64.deb ... 98s Unpacking libheif-plugin-libde265:arm64 (1.21.2-1) ... 98s Selecting previously unselected package libheif1:arm64. 98s Preparing to unpack .../40-libheif1_1.21.2-1_arm64.deb ... 98s Unpacking libheif1:arm64 (1.21.2-1) ... 98s Selecting previously unselected package libgomp1:arm64. 98s Preparing to unpack .../41-libgomp1_15.2.0-12ubuntu1_arm64.deb ... 98s Unpacking libgomp1:arm64 (15.2.0-12ubuntu1) ... 98s Selecting previously unselected package libimagequant0:arm64. 98s Preparing to unpack .../42-libimagequant0_2.18.0-1build1_arm64.deb ... 98s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 98s Selecting previously unselected package libjpeg-turbo8:arm64. 99s Preparing to unpack .../43-libjpeg-turbo8_2.1.5-4ubuntu2_arm64.deb ... 99s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 99s Selecting previously unselected package libjpeg8:arm64. 99s Preparing to unpack .../44-libjpeg8_8c-2ubuntu11_arm64.deb ... 99s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 99s Selecting previously unselected package libdeflate0:arm64. 99s Preparing to unpack .../45-libdeflate0_1.23-2_arm64.deb ... 99s Unpacking libdeflate0:arm64 (1.23-2) ... 99s Selecting previously unselected package libjbig0:arm64. 99s Preparing to unpack .../46-libjbig0_2.1-6.1ubuntu3_arm64.deb ... 99s Unpacking libjbig0:arm64 (2.1-6.1ubuntu3) ... 99s Selecting previously unselected package liblerc4:arm64. 99s Preparing to unpack .../47-liblerc4_4.0.0+ds-5ubuntu2_arm64.deb ... 99s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu2) ... 99s Selecting previously unselected package libwebp7:arm64. 99s Preparing to unpack .../48-libwebp7_1.5.0-0.1build1_arm64.deb ... 99s Unpacking libwebp7:arm64 (1.5.0-0.1build1) ... 99s Selecting previously unselected package libtiff6:arm64. 99s Preparing to unpack .../49-libtiff6_4.7.0-3ubuntu3_arm64.deb ... 99s Unpacking libtiff6:arm64 (4.7.0-3ubuntu3) ... 99s Selecting previously unselected package libxpm4:arm64. 99s Preparing to unpack .../50-libxpm4_1%3a3.5.17-1build3_arm64.deb ... 99s Unpacking libxpm4:arm64 (1:3.5.17-1build3) ... 99s Selecting previously unselected package libgd3:arm64. 99s Preparing to unpack .../51-libgd3_2.3.3-13ubuntu1_arm64.deb ... 99s Unpacking libgd3:arm64 (2.3.3-13ubuntu1) ... 99s Selecting previously unselected package libgvplugin-gd8:arm64. 99s Preparing to unpack .../52-libgvplugin-gd8_14.1.1-2ubuntu2_arm64.deb ... 99s Unpacking libgvplugin-gd8:arm64 (14.1.1-2ubuntu2) ... 99s Selecting previously unselected package fontconfig. 99s Preparing to unpack .../53-fontconfig_2.17.1-3ubuntu1_arm64.deb ... 99s Unpacking fontconfig (2.17.1-3ubuntu1) ... 99s Selecting previously unselected package libgraphite2-3:arm64. 99s Preparing to unpack .../54-libgraphite2-3_1.3.14-11ubuntu1_arm64.deb ... 99s Unpacking libgraphite2-3:arm64 (1.3.14-11ubuntu1) ... 99s Selecting previously unselected package libharfbuzz0b:arm64. 99s Preparing to unpack .../55-libharfbuzz0b_12.3.1-1_arm64.deb ... 99s Unpacking libharfbuzz0b:arm64 (12.3.1-1) ... 99s Selecting previously unselected package libthai-data. 99s Preparing to unpack .../56-libthai-data_0.1.30-1_all.deb ... 99s Unpacking libthai-data (0.1.30-1) ... 99s Selecting previously unselected package libdatrie1:arm64. 99s Preparing to unpack .../57-libdatrie1_0.2.14-1_arm64.deb ... 99s Unpacking libdatrie1:arm64 (0.2.14-1) ... 99s Selecting previously unselected package libthai0:arm64. 99s Preparing to unpack .../58-libthai0_0.1.30-1_arm64.deb ... 99s Unpacking libthai0:arm64 (0.1.30-1) ... 99s Selecting previously unselected package libpango-1.0-0:arm64. 99s Preparing to unpack .../59-libpango-1.0-0_1.57.0-1_arm64.deb ... 99s Unpacking libpango-1.0-0:arm64 (1.57.0-1) ... 99s Selecting previously unselected package libpangoft2-1.0-0:arm64. 99s Preparing to unpack .../60-libpangoft2-1.0-0_1.57.0-1_arm64.deb ... 99s Unpacking libpangoft2-1.0-0:arm64 (1.57.0-1) ... 99s Selecting previously unselected package libpangocairo-1.0-0:arm64. 99s Preparing to unpack .../61-libpangocairo-1.0-0_1.57.0-1_arm64.deb ... 99s Unpacking libpangocairo-1.0-0:arm64 (1.57.0-1) ... 99s Selecting previously unselected package libgvplugin-pango8:arm64. 99s Preparing to unpack .../62-libgvplugin-pango8_14.1.1-2ubuntu2_arm64.deb ... 99s Unpacking libgvplugin-pango8:arm64 (14.1.1-2ubuntu2) ... 99s Selecting previously unselected package graphviz. 99s Preparing to unpack .../63-graphviz_14.1.1-2ubuntu2_arm64.deb ... 99s Unpacking graphviz (14.1.1-2ubuntu2) ... 99s Selecting previously unselected package python3-pydot. 99s Preparing to unpack .../64-python3-pydot_4.0.1-1_all.deb ... 99s Unpacking python3-pydot (4.0.1-1) ... 99s Selecting previously unselected package python3-prov. 99s Preparing to unpack .../65-python3-prov_2.1.1-1_all.deb ... 99s Unpacking python3-prov (2.1.1-1) ... 100s Selecting previously unselected package python3-psutil. 100s Preparing to unpack .../66-python3-psutil_7.1.0-1ubuntu1_arm64.deb ... 100s Unpacking python3-psutil (7.1.0-1ubuntu1) ... 100s Selecting previously unselected package python3-rich-argparse. 100s Preparing to unpack .../67-python3-rich-argparse_1.6.0-2_all.deb ... 100s Unpacking python3-rich-argparse (1.6.0-2) ... 100s Selecting previously unselected package python3-spython. 100s Preparing to unpack .../68-python3-spython_0.3.13-2build1_all.deb ... 100s Unpacking python3-spython (0.3.13-2build1) ... 100s Selecting previously unselected package python3-arcp. 100s Preparing to unpack .../69-python3-arcp_0.2.1-7build1_all.deb ... 100s Unpacking python3-arcp (0.2.1-7build1) ... 100s Selecting previously unselected package cwltool. 100s Preparing to unpack .../70-cwltool_3.1.20251031082601-1_all.deb ... 100s Unpacking cwltool (3.1.20251031082601-1) ... 100s Selecting previously unselected package python3-wcwidth. 100s Preparing to unpack .../71-python3-wcwidth_0.2.14+dfsg1-1build1_all.deb ... 100s Unpacking python3-wcwidth (0.2.14+dfsg1-1build1) ... 100s Selecting previously unselected package python3-blessed. 100s Preparing to unpack .../72-python3-blessed_1.21.0-1_all.deb ... 100s Unpacking python3-blessed (1.21.0-1) ... 100s Selecting previously unselected package python3-configargparse. 100s Preparing to unpack .../73-python3-configargparse_1.7-2_all.deb ... 100s Unpacking python3-configargparse (1.7-2) ... 100s Selecting previously unselected package python3-dill. 100s Preparing to unpack .../74-python3-dill_0.4.0-1_all.deb ... 100s Unpacking python3-dill (0.4.0-1) ... 100s Selecting previously unselected package python3-docker. 100s Preparing to unpack .../75-python3-docker_7.1.0-2ubuntu1_all.deb ... 100s Unpacking python3-docker (7.1.0-2ubuntu1) ... 100s Selecting previously unselected package python3-prefixed. 100s Preparing to unpack .../76-python3-prefixed_0.7.0-1build1_all.deb ... 100s Unpacking python3-prefixed (0.7.0-1build1) ... 100s Selecting previously unselected package python3-enlighten. 100s Preparing to unpack .../77-python3-enlighten_1.11.2-1build1_arm64.deb ... 100s Unpacking python3-enlighten (1.11.2-1build1) ... 100s Selecting previously unselected package python3-prompt-toolkit. 100s Preparing to unpack .../78-python3-prompt-toolkit_3.0.52-2_all.deb ... 100s Unpacking python3-prompt-toolkit (3.0.52-2) ... 100s Selecting previously unselected package python3-pubsub. 100s Preparing to unpack .../79-python3-pubsub_4.0.3-7build1_all.deb ... 100s Unpacking python3-pubsub (4.0.3-7build1) ... 100s Selecting previously unselected package toil. 100s Preparing to unpack .../80-toil_9.1.0-1_all.deb ... 100s Unpacking toil (9.1.0-1) ... 100s Setting up libxdot4:arm64 (14.1.1-2ubuntu2) ... 100s Setting up libgraphite2-3:arm64 (1.3.14-11ubuntu1) ... 100s Setting up python3-configargparse (1.7-2) ... 100s Setting up python3-arcp (0.2.1-7build1) ... 101s Setting up libcdt6:arm64 (14.1.1-2ubuntu2) ... 101s Setting up libpixman-1-0:arm64 (0.46.4-1) ... 101s Setting up libsharpyuv0:arm64 (1.5.0-0.1build1) ... 101s Setting up libaom3:arm64 (3.13.1-2) ... 101s Setting up python3-filelock (3.20.3-1) ... 101s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu2) ... 101s Setting up libxpm4:arm64 (1:3.5.17-1build3) ... 101s Setting up libxrender1:arm64 (1:0.9.12-1) ... 101s Setting up libdatrie1:arm64 (0.2.14-1) ... 101s Setting up libxcb-render0:arm64 (1.17.0-2ubuntu1) ... 101s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 101s Setting up python3-mypy-extensions (1.1.0-1) ... 101s Setting up python3-docker (7.1.0-2ubuntu1) ... 101s Setting up python3-ruamel.yaml.clib (0.2.15+ds-1) ... 101s Setting up libdeflate0:arm64 (1.23-2) ... 101s Setting up libxcb-shm0:arm64 (1.17.0-2ubuntu1) ... 101s Setting up libgomp1:arm64 (15.2.0-12ubuntu1) ... 101s Setting up python3-networkx (3.2.1-4ubuntu2) ... 102s Setting up libjbig0:arm64 (2.1-6.1ubuntu3) ... 102s Setting up python3-psutil (7.1.0-1ubuntu1) ... 102s Setting up python3-prefixed (0.7.0-1build1) ... 103s Setting up python3-wcwidth (0.2.14+dfsg1-1build1) ... 103s Setting up python3-humanfriendly (10.0-6build1) ... 103s Setting up python3-spython (0.3.13-2build1) ... 103s Setting up libpathplan4:arm64 (14.1.1-2ubuntu2) ... 103s Setting up python3-dill (0.4.0-1) ... 103s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 103s Setting up fonts-dejavu-mono (2.37-8build1) ... 103s Setting up fonts-dejavu-core (2.37-8build1) ... 103s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 103s Setting up libltdl7:arm64 (2.5.4-9) ... 103s Setting up libcgraph8:arm64 (14.1.1-2ubuntu2) ... 103s Setting up libwebp7:arm64 (1.5.0-0.1build1) ... 103s Setting up python3-ruamel.yaml (0.18.10+ds-1build1) ... 103s Setting up python3-pubsub (4.0.3-7build1) ... 104s Setting up libgvpr2:arm64 (14.1.1-2ubuntu2) ... 104s Setting up python3-rich-argparse (1.6.0-2) ... 104s Setting up python3-rdflib (7.4.0-1) ... 104s Setting up libxslt1.1:arm64 (1.1.43-0.3) ... 104s Setting up libharfbuzz0b:arm64 (12.3.1-1) ... 104s Setting up libthai-data (0.1.30-1) ... 104s Setting up python3-msgpack (1.1.2-1) ... 104s Setting up python3-cachecontrol (0.14.3-1) ... 104s Setting up libde265-0:arm64 (1.0.16-1build1) ... 104s Setting up python3-argcomplete (3.6.3-1) ... 104s Setting up python3-coloredlogs (15.0.1-1build1) ... 105s Setting up python3-mistune (3.1.4-1) ... 105s Setting up libjs-bootstrap (3.4.1+dfsg-6) ... 105s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 105s Setting up python3-prompt-toolkit (3.0.52-2) ... 105s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 105s Setting up python3-blessed (1.21.0-1) ... 105s Setting up python3-schema-salad (8.9.20251102115403-1) ... 106s Setting up libthai0:arm64 (0.1.30-1) ... 106s Setting up python3-enlighten (1.11.2-1build1) ... 106s Setting up cwl-upgrader (1.2.14-1) ... 106s Setting up libgvc7:arm64 (14.1.1-2ubuntu2) ... 106s Setting up python3-lxml:arm64 (6.0.2-1) ... 106s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ... 106s Setting up libfontconfig1:arm64 (2.17.1-3ubuntu1) ... 106s Setting up fontconfig (2.17.1-3ubuntu1) ... 108s Regenerating fonts cache... done. 108s Setting up libpango-1.0-0:arm64 (1.57.0-1) ... 108s Setting up python3-cwl-utils (0.40-1) ... 111s Setting up libcairo2:arm64 (1.18.4-3) ... 111s Setting up libpangoft2-1.0-0:arm64 (1.57.0-1) ... 111s Setting up libpangocairo-1.0-0:arm64 (1.57.0-1) ... 111s Setting up libgvplugin-pango8:arm64 (14.1.1-2ubuntu2) ... 111s Setting up libheif-plugin-aomdec:arm64 (1.21.2-1) ... 111s Setting up libheif-plugin-libde265:arm64 (1.21.2-1) ... 111s Setting up libheif1:arm64 (1.21.2-1) ... 111s Setting up libgd3:arm64 (2.3.3-13ubuntu1) ... 111s Setting up libgvplugin-gd8:arm64 (14.1.1-2ubuntu2) ... 111s Setting up graphviz (14.1.1-2ubuntu2) ... 111s Setting up python3-pydot (4.0.1-1) ... 111s Setting up python3-prov (2.1.1-1) ... 111s Setting up cwltool (3.1.20251031082601-1) ... 111s Setting up toil (9.1.0-1) ... 112s Processing triggers for libc-bin (2.42-2ubuntu4) ... 112s Processing triggers for man-db (2.13.1-1) ... 114s autopkgtest [05:39:50]: test smoke-test: [----------------------- 114s Usage: toil COMMAND ... 114s toil --help 114s toil COMMAND --help 114s 114s Where COMMAND is one of the following: 114s 114s clean - Delete a job store used by a previous Toil workflow invocation. 114s config - Create a config file with all default Toil options. 114s debug-file - Debug tool for copying files contained in a toil jobStore. 114s debug-job - Debug tool for running a toil job locally. 114s destroy-cluster - Terminates the specified cluster and associated resources. 114s kill - Kills rogue toil processes. 114s launch-cluster - Launches a toil leader instance with the specified provisioner. 114s rsync-cluster - Rsyncs into the toil appliance container running on the leader of the cluster. 114s server - CLI entry for the Toil servers. 114s ssh-cluster - SSH into the toil appliance container running on the leader of the cluster. 114s stats - Reports statistical data about a given Toil workflow. 114s status - Tool for reporting on job status. 114s 115s WARNING: You are using cwltool version 3.1.20251031082601, which is not the version Toil is tested against. To install the correct cwltool for Toil, do: 115s 115s pip install cwltool==3.1.20250110105449 115s 115s usage: toil-cwl-runner [options] WORKFLOW [INFILE] [WF_OPTIONS...] 115s 115s positional arguments: 115s 115s WORKFLOW CWL file to run. 115s 115s INFILE YAML or JSON file of workflow inputs. 115s 115s WF_OPTIONS Additional inputs to the workflow as command-line 115s flags. If CWL workflow takes an input, the name of the 115s input can be used as an option. For example: 115s 115s toil-cwl-runner workflow.cwl --file1 file 115s 115s If an input has the same name as a Toil option, pass 115s '--' before it. 115s 115s options: 115s -h, --help show this help message and exit 115s --not-strict 115s --enable-dev Enable loading and running development versions of CWL 115s --enable-ext Enable loading and running 'cwltool:' extensions to 115s the CWL standards. 115s --quiet 115s --basedir BASEDIR 115s --outdir OUTDIR 115s --version show program's version number and exit 115s --log-dir LOG_DIR Log your tools stdout/stderr to this location outside 115s of container 115s --user-space-docker-cmd USER_SPACE_DOCKER_CMD 115s (Linux/OS X only) Specify a user space docker command 115s (like udocker or dx-docker) that will be used to call 115s 'pull' and 'run' 115s --singularity Use Singularity runtime for running containers. 115s Requires Singularity v2.6.1+ and Linux with kernel 115s version v3.18+ or with overlayfs support backported. 115s --podman Use Podman runtime for running containers. 115s --no-container Do not execute jobs in a Docker container, even when 115s `DockerRequirement` is specified under `hints`. 115s --leave-container Do not delete Docker container used by jobs after they 115s exit 115s --custom-net CUSTOM_NET 115s Specify docker network name to pass to docker run 115s command 115s --no-prepull Do not prepull the container prior to running the 115s workflow 115s --preserve-environment VAR1 VAR2 [VAR1 VAR2 ...] 115s Preserve specified environment variables when running 115s CommandLineTools 115s --preserve-entire-environment 115s Preserve all environment variable when running 115s CommandLineTools. 115s --beta-dependency-resolvers-configuration BETA_DEPENDENCY_RESOLVERS_CONFIGURATION 115s --beta-dependencies-directory BETA_DEPENDENCIES_DIRECTORY 115s --beta-use-biocontainers 115s --beta-conda-dependencies 115s --tmpdir-prefix TMPDIR_PREFIX 115s Path prefix for temporary directories 115s --tmp-outdir-prefix TMP_OUTDIR_PREFIX 115s Path prefix for intermediate output directories 115s --force-docker-pull Pull latest docker image even if it is locally present 115s --no-match-user Disable passing the current uid to `docker run --user` 115s --no-read-only Do not set root directory in the container as read- 115s only 115s --strict-memory-limit 115s When running with software containers and the Docker 115s engine, pass either the calculated memory allocation 115s from ResourceRequirements or the default of 1 gigabyte 115s to Docker's --memory option. 115s --strict-cpu-limit When running with software containers and the Docker 115s engine, pass either the calculated cpu allocation from 115s ResourceRequirements or the default of 1 core to 115s Docker's --cpu option. Requires docker version >= 115s v1.13. 115s --relax-path-checks Relax requirements on path names to permit spaces and 115s hash characters. 115s --default-container DEFAULT_CONTAINER 115s Specify a default docker container that will be used 115s if the workflow fails to specify one. 115s --compute-checksum Compute checksum of contents while collecting outputs 115s --no-compute-checksum 115s Do not compute checksum of contents while collecting 115s outputs 115s --eval-timeout EVAL_TIMEOUT 115s Time to wait for a Javascript expression to evaluate 115s before giving an error, default 20s. 115s --overrides OVERRIDES 115s Read process requirement overrides from file. 115s --mpi-config-file MPI_CONFIG_FILE 115s Platform specific configuration for MPI (parallel 115s launcher, its flag etc). See the cwltool README 115s section 'Running MPI-based tools' for details of the 115s format: https://github.com/common-workflow- 115s language/cwltool#running-mpi-based-tools-that-need-to- 115s be-launched 115s --bypass-file-store Do not use Toil's file store and assume all paths are 115s accessible in place from all nodes. 115s --reference-inputs Do not copy remote inputs into Toil's file store and 115s assume they are accessible in place from all nodes. 115s --disable-streaming Disable file streaming for files that have 115s 'streamable' flag True. 115s --cwl-default-ram Apply CWL specification default ramMin. 115s --no-cwl-default-ram Do not apply CWL specification default ramMin, so that 115s Toil --defaultMemory applies. This can help jobs get 115s to Slurm with no memory limit assigned. 115s --cwl-min-ram CWL_MIN_RAM 115s Specify a minimum memory allocation for all tasks .If 115s --no-cwl-default-ram is passed, this does not apply to 115s tools that do not specify a memory requirement; 115s --defaultMemory is used for those toolsin that case. 115s --destBucket DESTBUCKET 115s Specify a cloud bucket endpoint for output files. 115s --cachedir CACHEDIR Directory to cache intermediate workflow outputs to 115s avoid recomputing steps. Can be very helpful in the 115s development and troubleshooting of CWL documents. This 115s automatically bypasses the file store. Not to be 115s confused with --caching. 115s --runImportsOnWorkers, --run-imports-on-workers 115s Run the file imports on a worker instead of the 115s leader. This is useful if the leader is not optimized 115s for high network performance. If set to true, the 115s argument --importWorkersDisk must also be set. 115s --importWorkersBatchSize, --import-workers-batch-size IMPORT_WORKERS_BATCHSIZE 115s Specify the target total file size for file import 115s batches. As many files as can fit will go into each 115s batch import job. This should be set in conjunction 115s with the argument --runImportsOnWorkers. 115s --importWorkersDisk, --import-workers-disk IMPORT_WORKERS_DISK 115s Specify the disk size each import worker will get. 115s This usually will not need to be set as Toil will 115s attempt to use file streaming when downloading files. 115s If not possible, for example, when downloading from 115s AWS to a GCE job store, this should be set to the 115s largest file size of all files to import. This should 115s be set in conjunction with the arguments 115s --runImportsOnWorkers and --importWorkersBatchSize. 115s 115s --config PATH Get options from a config file. 115s 115s Logging Options: 115s --logCritical Set logging level to Critical. Default: INFO. 115s --logError Set logging level to Error. Default: INFO. 115s --logWarning Set logging level to Warning. Default: INFO. 115s --logInfo Set logging level to Info. Default: INFO. 115s --logDebug Set logging level to Debug. Default: INFO. 115s --logTrace Set logging level to Trace. Default: INFO. 115s --logOff Same as --logCritical. 115s --logLevel {Critical,Error,Warning,Info,Debug,Trace,critical,error,warning,info,debug,trace,CRITICAL,ERROR,WARNING,INFO,DEBUG,TRACE} 115s Set the log level. Default: INFO. Options: 115s ['Critical', 'Error', 'Warning', 'Info', 'Debug', 115s 'Trace', 'critical', 'error', 'warning', 'info', 115s 'debug', 'trace', 'CRITICAL', 'ERROR', 'WARNING', 115s 'INFO', 'DEBUG', 'TRACE']. 115s --logFile LOGFILE File to log in. 115s --rotatingLogging Turn on rotating logging, which prevents log files 115s from getting too big. 115s --logColors BOOL Enable or disable colored logging. Default: True 115s 115s Toil core options: 115s Options to specify the location of the Toil workflow and turn on stats collation about the performance of jobs. 115s 115s --jobstore, --jobStore JOBSTORE 115s The location of the job store for the workflow. A job 115s store holds persistent information about the jobs, 115s stats, and files in a workflow. If the workflow is run 115s with a distributed batch system, the job store must be 115s accessible by all worker nodes. Depending on the 115s desired job store implementation, the location should 115s be formatted according to one of the following 115s schemes: file: where points to a 115s directory on the file system aws:: 115s where is the name of an AWS region like us- 115s west-2 and will be prepended to the names of 115s any top-level AWS resources in use by job store, e.g. 115s S3 buckets. google:: TODO: explain 115s For backwards compatibility, you may also specify 115s ./foo (equivalent to file:./foo or just file:foo) or 115s /bar (equivalent to file:/bar). 115s --workDir PATH Absolute path to directory where temporary files 115s generated during the Toil run should be placed. 115s Standard output and error from batch system jobs 115s (unless --noStdOutErr is set) will be placed in this 115s directory. A cache directory may be placed in this 115s directory. Temp files and folders will be placed in a 115s directory toil- within workDir. The 115s workflowID is generated by Toil and will be reported 115s in the workflow logs. Default is determined by the 115s variables (TMPDIR, TEMP, TMP) via mkdtemp. This 115s directory needs to exist on all machines running jobs; 115s if capturing standard output and error from batch 115s system jobs is desired, it will generally need to be 115s on a shared file system. When sharing a cache between 115s containers on a host, this directory must be shared 115s between the containers. [env var: TOIL_WORKDIR] 115s --coordinationDir PATH 115s Absolute path to directory where Toil will keep state 115s and lock files. When sharing a cache between 115s containers on a host, this directory must be shared 115s between the containers. [env var: 115s TOIL_COORDINATION_DIR] 115s --noStdOutErr Do not capture standard output and error from batch 115s system jobs. 115s --stats Keep statistics about the toil workflow to be used by 115s 'toil stats'. 115s --clean {always,onError,never,onSuccess} 115s Determines the deletion of the jobStore upon 115s completion of the program. Choices: ['always', 115s 'onError', 'never', 'onSuccess']. The --stats option 115s requires information from the jobStore upon completion 115s so the jobStore will never be deleted with that flag. 115s If you wish to be able to restart the run, choose 115s 'never' or 'onSuccess'. Default is 'never' if stats is 115s enabled, and 'onSuccess' otherwise. 115s --cleanWorkDir {always,onError,never,onSuccess} 115s Determines deletion of temporary worker directory upon 115s completion of a job. Choices: ['always', 'onError', 115s 'never', 'onSuccess']. Default = always. WARNING: This 115s option should be changed for debugging only. Running a 115s full pipeline with this option could fill your disk 115s with excessive intermediate data. 115s --clusterStats [OPT_PATH] 115s If enabled, writes out JSON resource usage statistics 115s to a file. The default location for this file is the 115s current working directory, but an absolute path can 115s also be passed to specify where this file should be 115s written. This options only applies when using scalable 115s batch systems. 115s 115s Toil options for restarting an existing workflow: 115s Allows the restart of an existing workflow 115s 115s --restart If --restart is specified then will attempt to restart 115s existing workflow at the location pointed to by the 115s --jobStore option. Will raise an exception if the 115s workflow does not exist 115s 115s Toil options for specifying the batch system: 115s Allows the specification of the batch system. 115s 115s --batchSystem {aws_batch,single_machine,grid_engine,lsf,mesos,slurm,torque,htcondor,kubernetes} 115s The type of batch system to run the job(s) with, 115s currently can be one of aws_batch, single_machine, 115s grid_engine, lsf, mesos, slurm, torque, htcondor, 115s kubernetes. Default = single_machine 115s --disableHotDeployment 115s Hot-deployment was renamed to auto-deployment. Option 115s now redirects to --disableAutoDeployment. Left in for 115s backwards compatibility. 115s --disableAutoDeployment DISABLEAUTODEPLOYMENT 115s Should auto-deployment of Toil Python workflows be 115s deactivated? If True, the workflow's Python code 115s should be present at the same location on all workers. 115s Default = False. 115s --maxJobs MAX_JOBS Specifies the maximum number of jobs to submit to the 115s backing scheduler at once. Not supported on Mesos or 115s AWS Batch. Use 0 for unlimited. Defaults to unlimited. 115s --maxLocalJobs MAX_LOCAL_JOBS 115s Specifies the maximum number of housekeeping jobs to 115s run sumultaneously on the local system. Use 0 for 115s unlimited. Defaults to the number of local cores (4). 115s --manualMemArgs Do not add the default arguments: 'hv=MEMORY' & 115s 'h_vmem=MEMORY' to the qsub call, and instead rely on 115s TOIL_GRIDGENGINE_ARGS to supply alternative arguments. 115s Requires that TOIL_GRIDGENGINE_ARGS be set. 115s --runLocalJobsOnWorkers, --runCwlInternalJobsOnWorkers 115s Whether to run jobs marked as local (e.g. CWLScatter) 115s on the worker nodes instead of the leader node. If 115s false (default), then all such jobs are run on the 115s leader node. Setting this to true can speed up CWL 115s pipelines for very large workflows with many sub- 115s workflows and/or scatters, provided that the worker 115s pool is large enough. 115s --coalesceStatusCalls 115s Ask for job statuses from the batch system in a batch. 115s Deprecated; now always enabled where supported. 115s --statePollingWait STATEPOLLINGWAIT 115s Time, in seconds, to wait before doing a scheduler 115s query for job state. Return cached results if within 115s the waiting period. Only works for grid engine batch 115s systems such as gridengine, htcondor, torque, slurm, 115s and lsf. 115s --statePollingTimeout STATE_POLLING_TIMEOUT 115s Time, in seconds, to retry against a broken scheduler. 115s Only works for grid engine batch systems such as 115s gridengine, htcondor, torque, slurm, and lsf. 115s --batchLogsDir BATCH_LOGS_DIR 115s Directory to tell the backing batch system to log 115s into. Should be available on both the leader and the 115s workers, if the backing batch system writes logs to 115s the worker machines' filesystems, as many HPC 115s schedulers do. If unset, the Toil work directory will 115s be used. Only works for grid engine batch systems such 115s as gridengine, htcondor, torque, slurm, and lsf. [env 115s var: TOIL_BATCH_LOGS_DIR] 115s --memoryIsProduct If the batch system understands requested memory as a 115s product of the requested memory and the numberof 115s cores, set this flag to properly allocate memory. 115s --awsBatchRegion AWS_BATCH_REGION 115s The AWS region containing the AWS Batch queue to 115s submit to. [env var: TOIL_AWS_REGION] 115s --awsBatchQueue AWS_BATCH_QUEUE 115s The name or ARN of the AWS Batch queue to submit to. 115s [env var: TOIL_AWS_BATCH_QUEUE] 115s --awsBatchJobRoleArn AWS_BATCH_JOB_ROLE_ARN 115s The ARN of an IAM role to run AWS Batch jobs as, so 115s they can e.g. access a job store. Must be assumable by 115s ecs-tasks.amazonaws.com. [env var: 115s TOIL_AWS_BATCH_JOB_ROLE_ARN] 115s --scale SCALE A scaling factor to change the value of all submitted 115s tasks's submitted cores. Used in the single_machine 115s batch system. Useful for running workflows on smaller 115s machines than they were designed for, by setting a 115s value less than 1. (default: 1) 115s --slurmAllocateMem SLURM_ALLOCATE_MEM 115s If False, do not use --mem. Used as a workaround for 115s Slurm clusters that reject jobs with memory 115s allocations. [env var: TOIL_SLURM_ALLOCATE_MEM] 115s --slurmDefaultAllMem SLURM_DEFAULT_ALL_MEM 115s If True, assign Toil jobs without their own memory 115s requirements all available memory on a Slurm node (via 115s Slurm --mem=0). [env var: TOIL_SLURM_DEFAULT_ALL_MEM] 115s --slurmTime SLURM_TIME 115s Slurm job time limit, in [DD-]HH:MM:SS format. [env 115s var: TOIL_SLURM_TIME] 115s --slurmPartition SLURM_PARTITION 115s Partition to send Slurm jobs to. [env var: 115s TOIL_SLURM_PARTITION] 115s --slurmGPUPartition SLURM_GPU_PARTITION 115s Partition to send Slurm jobs to if they ask for GPUs. 115s [env var: TOIL_SLURM_GPU_PARTITION] 115s --slurmPE SLURM_PE Special partition to send Slurm jobs to if they ask 115s for more than 1 CPU. [env var: TOIL_SLURM_PE] 115s --slurmArgs SLURM_ARGS 115s Extra arguments to pass to Slurm. [env var: 115s TOIL_SLURM_ARGS] 115s 115s Toil options for configuring storage: 115s Allows configuring Toil's data storage. 115s 115s --symlinkImports BOOL 115s When using a filesystem based job store, CWL input 115s files are by default symlinked in. Setting this option 115s to True instead copies the files into the job store, 115s which may protect them from being modified externally. 115s When set to False, as long as caching is enabled, Toil 115s will protect the file automatically by changing the 115s permissions to read-only. default=True 115s --moveOutputs BOOL When using a filesystem based job store, output files 115s are by default moved to the output directory, and a 115s symlink to the moved exported file is created at the 115s initial location. Setting this option to True instead 115s copies the files into the output directory. Applies to 115s filesystem-based job stores only. default=False 115s --caching BOOL Enable or disable worker level file caching for your 115s workflow, specifying this overrides default from batch 115s system. Does not affect CWL or WDL task caching. 115s --symlinkJobStoreReads BOOL 115s Allow reads and container mounts from a JobStore's 115s shared filesystem directly via symlink. default=True 115s 115s Toil options for autoscaling the cluster of worker nodes: 115s Allows the specification of the minimum and maximum number of nodes in an autoscaled cluster, as well as parameters to control the level of provisioning. 115s 115s --provisioner, -p {aws,gce,None} 115s The provisioner for cluster auto-scaling. This is the 115s main Toil '--provisioner' option, and defaults to None 115s for running on single machine and non-auto-scaling 115s batch systems. The currently supported choices are 115s ['aws', 'gce', None]. The default is None. 115s --nodeTypes NODETYPES 115s Specifies a list of comma-separated node types, each 115s of which is composed of slash-separated instance 115s types, and an optional spot bid set off by a colon, 115s making the node type preemptible. Instance types may 115s appear in multiple node types, and the same node type 115s may appear as both preemptible and non-preemptible. 115s Valid argument specifying two node types: 115s c5.4xlarge/c5a.4xlarge:0.42,t2.large Node types: 115s c5.4xlarge/c5a.4xlarge:0.42 and t2.large Instance 115s types: c5.4xlarge, c5a.4xlarge, and t2.large 115s Semantics: Bid $0.42/hour for either c5.4xlarge or 115s c5a.4xlarge instances, treated interchangeably, while 115s they are available at that price, and buy t2.large 115s instances at full price. default=[] 115s --maxNodes INT[,INT...] 115s Maximum number of nodes of each type in the cluster, 115s if using autoscaling, provided as a comma-separated 115s list. The first value is used as a default if the list 115s length is less than the number of nodeTypes. 115s default=[10] 115s --minNodes INT[,INT...] 115s Mininum number of nodes of each type in the cluster, 115s if using auto-scaling. This should be provided as a 115s comma-separated list of the same length as the list of 115s node types. default=[0] 115s --targetTime INT Sets how rapidly you aim to complete jobs in seconds. 115s Shorter times mean more aggressive parallelization. 115s The autoscaler attempts to scale up/down so that it 115s expects all queued jobs will complete within 115s targetTime seconds. default=1800 115s --betaInertia FLOAT A smoothing parameter to prevent unnecessary 115s oscillations in the number of provisioned nodes. This 115s controls an exponentially weighted moving average of 115s the estimated number of nodes. A value of 0.0 disables 115s any smoothing, and a value of 0.9 will smooth so much 115s that few changes will ever be made. Must be between 115s 0.0 and 0.9. default=0.1 115s --scaleInterval INT The interval (seconds) between assessing if the scale 115s of the cluster needs to change. default=60 115s --preemptibleCompensation, --preemptableCompensation FLOAT 115s The preference of the autoscaler to replace 115s preemptible nodes with non-preemptible nodes, when 115s preemptible nodes cannot be started for some reason. 115s This value must be between 0.0 and 1.0, inclusive. A 115s value of 0.0 disables such compensation, a value of 115s 0.5 compensates two missing preemptible nodes with a 115s non-preemptible one. A value of 1.0 replaces every 115s missing pre-emptable node with a non-preemptible one. 115s default=0.0 115s --nodeStorage INT Specify the size of the root volume of worker nodes 115s when they are launched in gigabytes. You may want to 115s set this if your jobs require a lot of disk space. 115s (default=50). 115s --nodeStorageOverrides NODETYPE:NODESTORAGE[,NODETYPE:NODESTORAGE...] 115s Comma-separated list of nodeType:nodeStorage that are 115s used to override the default value from --nodeStorage 115s for the specified nodeType(s). This is useful for 115s heterogeneous jobs where some tasks require much more 115s disk than others. 115s --metrics BOOL Enable the prometheus/grafana dashboard for monitoring 115s CPU/RAM usage, queue size, and issued jobs. 115s --assumeZeroOverhead BOOL 115s Ignore scheduler and OS overhead and assume jobs can 115s use every last byte of memory and disk on a node when 115s autoscaling. 115s 115s Toil options for cores/memory requirements: 115s The options to specify default cores/memory requirements (if not specified by the jobs themselves), and to limit the total amount of memory/cores requested from the batch system. 115s 115s --defaultMemory DEFAULTMEMORY 115s The default amount of memory to request for a job. 115s Only applicable to jobs that do not specify an 115s explicit value for this requirement. Standard suffixes 115s like K, Ki, M, Mi, G or Gi are supported. Default is 115s 2.0 Gi. 115s --defaultCores FLOAT The default amount of cpu to request for a job. Only 115s applicable to jobs that do not specify an explicit 115s value for this requirement. Fractions of a core (for 115s example 0.1) are supported on some batch systems 115s [mesos, single_machine]. Default is 1. 115s --defaultDisk INT The default amount of disk to request for a job. Only 115s applicable to jobs that do not specify an explicit 115s value for this requirement. Standard suffixes like K, 115s Ki, M, Mi, G or Gi are supported. Default is 2.0 Gi. 115s --defaultAccelerators ACCELERATOR[,ACCELERATOR...] 115s The default amount of accelerators to request for a 115s job. Only applicable to jobs that do not specify an 115s explicit value for this requirement. Each accelerator 115s specification can have a type (gpu [default], nvidia, 115s amd, cuda, rocm, opencl, or a specific model like 115s nvidia-tesla-k80), and a count [default: 1]. If both a 115s type and a count are used, they must be separated by a 115s colon. If multiple types of accelerators are used, the 115s specifications are separated by commas. Default is []. 115s --defaultPreemptible, --defaultPreemptable [BOOL] 115s Make all jobs able to run on preemptible (spot) nodes 115s by default. 115s --maxCores INT The max amount of cpu to request for a job. Only 115s applicable to jobs that do not specify an explicit 115s value for this requirement. Fractions of a core (for 115s example 0.1) are supported on some batch systems 115s [mesos, single_machine]. Default is 115s 9223372036854775807. 115s --maxMemory INT The max amount of memory to request for a job. Only 115s applicable to jobs that do not specify an explicit 115s value for this requirement. Standard suffixes like K, 115s Ki, M, Mi, G or Gi are supported. Default is 8.0 Ei. 115s --maxDisk INT The max amount of disk to request for a job. Only 115s applicable to jobs that do not specify an explicit 115s value for this requirement. Standard suffixes like K, 115s Ki, M, Mi, G or Gi are supported. Default is 8.0 Ei. 115s 115s Toil options for rescuing/killing/restarting jobs: 115s The options for jobs that either run too long/fail or get lost (some batch systems have issues!). 115s 115s --retryCount INT Number of times to retry a failing job before giving 115s up and labeling job failed. default=1 115s --stopOnFirstFailure BOOL 115s Stop the workflow at the first complete job failure. 115s --enableUnlimitedPreemptibleRetries, --enableUnlimitedPreemptableRetries BOOL 115s If set, preemptible failures (or any failure due to an 115s instance getting unexpectedly terminated) will not 115s count towards job failures and --retryCount. 115s --doubleMem BOOL If set, batch jobs which die to reaching memory limit 115s on batch schedulers will have their memory doubled and 115s they will be retried. The remaining retry count will 115s be reduced by 1. Currently supported by LSF. 115s --maxJobDuration INT Maximum runtime of a job (in seconds) before we kill 115s it (this is a lower bound, and the actual time before 115s killing the job may be longer). 115s default=9223372036854775807 115s --rescueJobsFrequency INT 115s Period of time to wait (in seconds) between checking 115s for missing/overlong jobs, that is jobs which get lost 115s by the batch system. Expert parameter. default=60 115s --jobStoreTimeout FLOAT 115s Maximum time (in seconds) to wait for a job's update 115s to the job store before declaring it failed. 115s default=30 115s 115s Toil log management options: 115s Options for how Toil should manage its logs. 115s 115s --maxLogFileSize MAXLOGFILESIZE 115s The maximum size of a job log file to keep (in bytes), 115s log files larger than this will be truncated to the 115s last X bytes. Setting this option to zero will prevent 115s any truncation. Setting this option to a negative 115s value will truncate from the beginning. Default=100.0 115s Mi 115s --writeLogs [OPT_PATH] 115s Write worker logs received by the leader into their 115s own files at the specified path. Any non-empty 115s standard output and error from failed batch system 115s jobs will also be written into files at this path. The 115s current working directory will be used if a path is 115s not specified explicitly. Note: By default only the 115s logs of failed jobs are returned to leader. Set log 115s level to 'debug' or enable '--writeLogsFromAllJobs' to 115s get logs back from successful jobs, and adjust 115s 'maxLogFileSize' to control the truncation limit for 115s worker logs. 115s --writeLogsGzip [OPT_PATH] 115s Identical to --writeLogs except the logs files are 115s gzipped on the leader. 115s --writeLogsFromAllJobs BOOL 115s Whether to write logs from all jobs (including the 115s successful ones) without necessarily setting the log 115s level to 'debug'. Ensure that either --writeLogs or 115s --writeLogsGzip is set if enabling this option. 115s --writeMessages PATH File to send messages from the leader's message bus 115s to. 115s --realTimeLogging BOOL 115s Enable real-time logging from workers to leader 115s 115s Toil miscellaneous options: 115s Everything else. 115s 115s --disableChaining BOOL 115s Disables chaining of jobs (chaining uses one job's 115s resource allocation for its successor job if 115s possible). 115s --disableJobStoreChecksumVerification BOOL 115s Disables checksum verification for files transferred 115s to/from the job store. Checksum verification is a 115s safety check to ensure the data is not corrupted 115s during transfer. Currently only supported for non- 115s streaming AWS files. 115s --sseKey PATH Path to file containing 32 character key to be used 115s for server-side encryption on awsJobStore or 115s googleJobStore. SSE will not be used if this flag is 115s not passed. 115s --setEnv, -e NAME=VALUE or NAME 115s Set an environment variable early on in the worker. If 115s VALUE is null, it will be looked up in the current 115s environment. Independently of this option, the worker 115s will try to emulate the leader's environment before 115s running a job, except for some variables known to vary 115s across systems. Using this option, a variable can be 115s injected into the worker process itself before it is 115s started. 115s --servicePollingInterval FLOAT 115s Interval of time service jobs wait between polling for 115s the existence of the keep-alive flag. Default: 60.0 115s --forceDockerAppliance BOOL 115s Disables sanity checking the existence of the docker 115s image specified by TOIL_APPLIANCE_SELF, which Toil 115s uses to provision mesos for autoscaling. 115s --statusWait INT Seconds to wait between reports of running jobs. 115s --disableProgress Disables the progress bar shown when standard error is 115s a terminal. 115s --publishWorkflowMetrics {all,current,no} 115s Whether to publish workflow metrics reports (including 115s unique workflow and task run IDs, job names, and 115s version and Toil feature use information) to Dockstore 115s when a workflow completes. Selecting "current" will 115s publish metrics for the current workflow. Selecting 115s "all" will also publish prior workflow runs from the 115s Toil history database, even if they themselves were 115s run with "no". Note that once published, workflow 115s metrics CANNOT be deleted or un-published; they will 115s stay published forever! 115s 115s Toil debug options: 115s Debug options for finding problems or helping with testing. 115s 115s --debugWorker Experimental no forking mode for local debugging. 115s Specifically, workers are not forked and stderr/stdout 115s are not redirected to the log. 115s --disableWorkerOutputCapture 115s Let worker output go to worker's standard out/error 115s instead of per-job logs. 115s --badWorker FLOAT For testing purposes randomly kill --badWorker 115s proportion of jobs using SIGKILL. default=0.0 115s --badWorkerFailInterval FLOAT 115s When killing the job pick uniformly within the 115s interval from 0.0 to --badWorkerFailInterval seconds 115s after the worker starts. default=0.01 115s 115s Options for recording the Docker container identifier into a file.: 115s --cidfile-dir CIDFILE_DIR 115s Store the Docker container ID into a file in the 115s specified directory. 115s --cidfile-prefix CIDFILE_PREFIX 115s Specify a prefix to the container ID filename. Final 115s file name will be followed by a timestamp. The default 115s is no prefix. 115s 115s Options for recording provenance information of the execution: 115s --provenance PROVENANCE 115s Save provenance to specified folder as a Research 115s Object that captures and aggregates workflow execution 115s and data products. 115s --enable-user-provenance 115s Record user account info as part of provenance. 115s --disable-user-provenance 115s Do not record user account info in provenance. 115s --enable-host-provenance 115s Record host info as part of provenance. 115s --disable-host-provenance 115s Do not record host info in provenance. 115s --orcid ORCID Record user ORCID identifier as part of provenance, 115s e.g. https://orcid.org/0000-0002-1825-0097 or 115s 0000-0002-1825-0097. Alternatively the environment 115s variable ORCID may be set. 115s --full-name CWL_FULL_NAME 115s Record full name of user as part of provenance, e.g. 115s Josiah Carberry. You may need to use shell quotes to 115s preserve spaces. Alternatively the environment 115s variable CWL_FULL_NAME may be set. 115s 115s Args that start with '--' can also be set in a config file 115s (/home/ubuntu/.toil/default.yaml or specified via --config). The config file 115s uses YAML syntax and must represent a YAML 'mapping' (for details, see 115s http://learn.getgrav.org/advanced/yaml). In general, command-line values 115s override environment variables which override config file values which 115s override defaults. 116s autopkgtest [05:39:52]: test smoke-test: -----------------------] 116s autopkgtest [05:39:52]: test smoke-test: - - - - - - - - - - results - - - - - - - - - - 116s smoke-test PASS (superficial) 116s autopkgtest [05:39:52]: test pybuild-autopkgtest: preparing testbed 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s Solving dependencies... 117s The following NEW packages will be installed: 117s autoconf automake autopoint autotools-dev build-essential containerd cpp 117s cpp-15 cpp-15-aarch64-linux-gnu cpp-aarch64-linux-gnu cwl-utils cwltest 117s cwltool-doc debhelper debugedit dh-autoreconf dh-python 117s dh-strip-nondeterminism docker.io docutils-common dwz fonts-font-awesome 117s fonts-lato g++ g++-15 g++-15-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 117s gcc-15 gcc-15-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext 117s intltool-debian libarchive-zip-perl libasan8 libcc1-0 libdebhelper-perl 117s libfile-stripnondeterminism-perl libgcc-15-dev libhwasan0 libisl23 libitm1 117s libjs-jquery libjs-underscore libjson-perl liblsan0 libmpc3 117s libpython3.14-minimal libpython3.14-stdlib libstdc++-15-dev libtool libtsan2 117s libubsan1 m4 po-debconf pybuild-plugin-autopkgtest pybuild-plugin-pyproject 117s python3-alabaster python3-all python3-antlr4 python3-astroid python3-build 117s python3-defusedxml python3-doc python3-docutils python3-execnet 117s python3-imagesize python3-iniconfig python3-installer python3-junit.xml 117s python3-pluggy python3-pyproject-hooks python3-pytest 117s python3-pytest-httpserver python3-pytest-timeout python3-pytest-xdist 117s python3-pytz python3-roman-numerals python3-setuptools-scm 117s python3-snowballstemmer python3-sphinx python3-sphinx-autoapi 117s python3-sphinx-autodoc-typehints python3-sphinxcontrib.autoprogram 117s python3-stubserver python3-tz python3-wdlparse python3-werkzeug 117s python3-wheel python3.13-doc python3.14 python3.14-minimal runc sgml-base 117s sphinx-common sphinx-rtd-theme-common xml-core 117s 0 upgraded, 97 newly installed, 0 to remove and 0 not upgraded. 117s Need to get 164 MB of archives. 117s After this operation, 642 MB of additional disk space will be used. 117s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-lato all 2.015-1build1 [2779 kB] 118s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-minimal arm64 3.14.2-1 [917 kB] 118s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-minimal arm64 3.14.2-1 [2548 kB] 118s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 m4 arm64 1.4.20-2 [213 kB] 118s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 autoconf all 2.72-3.1ubuntu1 [384 kB] 118s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 autotools-dev all 20240727.1 [43.4 kB] 118s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 automake all 1:1.18.1-3build1 [582 kB] 118s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 autopoint all 0.23.2-1 [620 kB] 118s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libisl23 arm64 0.27-1build1 [676 kB] 118s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libmpc3 arm64 1.3.1-2 [55.6 kB] 118s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [11.7 MB] 118s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15 arm64 15.2.0-12ubuntu1 [1030 B] 118s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [5736 B] 118s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp arm64 4:15.2.0-4ubuntu1 [22.4 kB] 118s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libcc1-0 arm64 15.2.0-12ubuntu1 [49.0 kB] 118s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libitm1 arm64 15.2.0-12ubuntu1 [27.8 kB] 118s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libasan8 arm64 15.2.0-12ubuntu1 [2920 kB] 118s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 liblsan0 arm64 15.2.0-12ubuntu1 [1316 kB] 119s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libtsan2 arm64 15.2.0-12ubuntu1 [2688 kB] 119s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libubsan1 arm64 15.2.0-12ubuntu1 [1175 kB] 119s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libhwasan0 arm64 15.2.0-12ubuntu1 [1638 kB] 119s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-15-dev arm64 15.2.0-12ubuntu1 [2600 kB] 119s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [23.1 MB] 120s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15 arm64 15.2.0-12ubuntu1 [519 kB] 120s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1206 B] 120s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc arm64 4:15.2.0-4ubuntu1 [5016 B] 120s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libstdc++-15-dev arm64 15.2.0-12ubuntu1 [2549 kB] 120s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [13.2 MB] 120s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15 arm64 15.2.0-12ubuntu1 [25.3 kB] 120s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [956 B] 120s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 g++ arm64 4:15.2.0-4ubuntu1 [1080 B] 120s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 build-essential arm64 12.12ubuntu2 [5254 B] 120s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 runc arm64 1.4.0-0ubuntu1 [8898 kB] 121s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 containerd arm64 2.2.1-0ubuntu1 [25.0 MB] 121s Get:35 http://ftpmaster.internal/ubuntu resolute/universe arm64 cwl-utils all 0.40-1 [2578 B] 121s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-defusedxml all 0.7.1-3build1 [42.4 kB] 121s Get:37 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-junit.xml all 1.9-6 [9062 B] 121s Get:38 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 2.1.0-2 [6962 B] 121s Get:39 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pluggy all 1.6.0-2 [21.1 kB] 121s Get:40 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest all 9.0.2-2 [277 kB] 122s Get:41 http://ftpmaster.internal/ubuntu resolute/universe arm64 cwltest all 2.6.20251216093331-1 [29.1 kB] 122s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 122s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB] 122s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 122s Get:45 http://ftpmaster.internal/ubuntu resolute/universe arm64 cwltool-doc all 3.1.20251031082601-1 [332 kB] 122s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 122s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libtool all 2.5.4-9 [169 kB] 122s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 dh-autoreconf all 21 [12.5 kB] 122s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 122s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 122s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 122s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 debugedit arm64 1:5.2-3 [49.1 kB] 122s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 dwz arm64 0.16-2 [113 kB] 122s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 gettext arm64 0.23.2-1 [998 kB] 122s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 122s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 po-debconf all 1.0.22 [215 kB] 122s Get:57 http://ftpmaster.internal/ubuntu resolute/main arm64 debhelper all 13.28ubuntu1 [916 kB] 122s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 dh-python all 7.20260125 [122 kB] 122s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 docker.io arm64 29.1.3-0ubuntu1 [31.9 MB] 123s Get:60 http://ftpmaster.internal/ubuntu resolute/main arm64 sgml-base all 1.31+nmu1 [11.0 kB] 123s Get:61 http://ftpmaster.internal/ubuntu resolute/main arm64 xml-core all 0.19build1 [20.3 kB] 123s Get:62 http://ftpmaster.internal/ubuntu resolute/main arm64 docutils-common all 0.22.4+dfsg-1 [130 kB] 123s Get:63 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-underscore all 1.13.7~dfsg+~1.13.0-1 [86.4 kB] 123s Get:64 http://ftpmaster.internal/ubuntu resolute/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 123s Get:65 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-stdlib arm64 3.14.2-1 [2351 kB] 123s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 pybuild-plugin-autopkgtest all 7.20260125 [1744 B] 123s Get:67 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 123s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-wheel all 0.46.1-2 [22.1 kB] 123s Get:69 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-build all 1.2.2-5 [30.9 kB] 123s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 123s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 pybuild-plugin-pyproject all 7.20260125 [1712 B] 123s Get:72 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14 arm64 3.14.2-1 [816 kB] 123s Get:73 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-all arm64 3.13.9-3 [890 B] 123s Get:74 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-antlr4 all 4.9.2-1build1 [99.1 kB] 123s Get:75 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-astroid all 4.0.2-1ubuntu1 [172 kB] 123s Get:76 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13-doc all 3.13.11-1 [14.3 MB] 123s Get:77 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-doc all 3.13.9-3 [11.1 kB] 123s Get:78 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-roman-numerals all 4.1.0-1 [8660 B] 123s Get:79 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-docutils all 0.22.4+dfsg-1 [439 kB] 123s Get:80 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-execnet all 2.1.1-1build1 [33.5 kB] 123s Get:81 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-imagesize all 1.4.1-1build1 [6900 B] 123s Get:82 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-werkzeug all 3.1.5-1 [170 kB] 123s Get:83 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest-httpserver all 1.1.3-1 [19.1 kB] 123s Get:84 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest-timeout all 2.4.0-2 [22.5 kB] 123s Get:85 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest-xdist all 3.8.0-4 [34.7 kB] 123s Get:86 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytz all 2025.2-5 [32.4 kB] 123s Get:87 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-setuptools-scm all 8.2.1-4 [32.8 kB] 123s Get:88 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-snowballstemmer all 3.0.1-1 [65.9 kB] 123s Get:89 http://ftpmaster.internal/ubuntu resolute/main arm64 sphinx-common all 8.2.3-12 [657 kB] 123s Get:90 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-alabaster all 0.7.16-0.1build1 [18.6 kB] 123s Get:91 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-sphinx all 8.2.3-12 [483 kB] 123s Get:92 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sphinx-autoapi all 3.6.1-1 [102 kB] 123s Get:93 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sphinx-autodoc-typehints all 3.5.2-1 [22.7 kB] 123s Get:94 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sphinxcontrib.autoprogram all 0.1.9-1 [9566 B] 123s Get:95 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-stubserver all 1.1-4build1 [7994 B] 123s Get:96 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-tz all 2025.2-5 [1760 B] 123s Get:97 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-wdlparse all 0.1.0-3build1 [71.0 kB] 124s Preconfiguring packages ... 124s Fetched 164 MB in 6s (27.0 MB/s) 124s Selecting previously unselected package fonts-lato. 124s (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 ... 143596 files and directories currently installed.) 124s Preparing to unpack .../00-fonts-lato_2.015-1build1_all.deb ... 124s Unpacking fonts-lato (2.015-1build1) ... 124s Selecting previously unselected package libpython3.14-minimal:arm64. 124s Preparing to unpack .../01-libpython3.14-minimal_3.14.2-1_arm64.deb ... 124s Unpacking libpython3.14-minimal:arm64 (3.14.2-1) ... 124s Selecting previously unselected package python3.14-minimal. 124s Preparing to unpack .../02-python3.14-minimal_3.14.2-1_arm64.deb ... 124s Unpacking python3.14-minimal (3.14.2-1) ... 124s Selecting previously unselected package m4. 124s Preparing to unpack .../03-m4_1.4.20-2_arm64.deb ... 124s Unpacking m4 (1.4.20-2) ... 124s Selecting previously unselected package autoconf. 124s Preparing to unpack .../04-autoconf_2.72-3.1ubuntu1_all.deb ... 124s Unpacking autoconf (2.72-3.1ubuntu1) ... 124s Selecting previously unselected package autotools-dev. 124s Preparing to unpack .../05-autotools-dev_20240727.1_all.deb ... 124s Unpacking autotools-dev (20240727.1) ... 124s Selecting previously unselected package automake. 124s Preparing to unpack .../06-automake_1%3a1.18.1-3build1_all.deb ... 124s Unpacking automake (1:1.18.1-3build1) ... 124s Selecting previously unselected package autopoint. 124s Preparing to unpack .../07-autopoint_0.23.2-1_all.deb ... 124s Unpacking autopoint (0.23.2-1) ... 124s Selecting previously unselected package libisl23:arm64. 124s Preparing to unpack .../08-libisl23_0.27-1build1_arm64.deb ... 124s Unpacking libisl23:arm64 (0.27-1build1) ... 125s Selecting previously unselected package libmpc3:arm64. 125s Preparing to unpack .../09-libmpc3_1.3.1-2_arm64.deb ... 125s Unpacking libmpc3:arm64 (1.3.1-2) ... 125s Selecting previously unselected package cpp-15-aarch64-linux-gnu. 125s Preparing to unpack .../10-cpp-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 125s Unpacking cpp-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 125s Selecting previously unselected package cpp-15. 125s Preparing to unpack .../11-cpp-15_15.2.0-12ubuntu1_arm64.deb ... 125s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 125s Selecting previously unselected package cpp-aarch64-linux-gnu. 125s Preparing to unpack .../12-cpp-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 125s Unpacking cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 125s Selecting previously unselected package cpp. 125s Preparing to unpack .../13-cpp_4%3a15.2.0-4ubuntu1_arm64.deb ... 125s Unpacking cpp (4:15.2.0-4ubuntu1) ... 125s Selecting previously unselected package libcc1-0:arm64. 125s Preparing to unpack .../14-libcc1-0_15.2.0-12ubuntu1_arm64.deb ... 125s Unpacking libcc1-0:arm64 (15.2.0-12ubuntu1) ... 125s Selecting previously unselected package libitm1:arm64. 125s Preparing to unpack .../15-libitm1_15.2.0-12ubuntu1_arm64.deb ... 125s Unpacking libitm1:arm64 (15.2.0-12ubuntu1) ... 125s Selecting previously unselected package libasan8:arm64. 125s Preparing to unpack .../16-libasan8_15.2.0-12ubuntu1_arm64.deb ... 125s Unpacking libasan8:arm64 (15.2.0-12ubuntu1) ... 125s Selecting previously unselected package liblsan0:arm64. 125s Preparing to unpack .../17-liblsan0_15.2.0-12ubuntu1_arm64.deb ... 125s Unpacking liblsan0:arm64 (15.2.0-12ubuntu1) ... 125s Selecting previously unselected package libtsan2:arm64. 125s Preparing to unpack .../18-libtsan2_15.2.0-12ubuntu1_arm64.deb ... 125s Unpacking libtsan2:arm64 (15.2.0-12ubuntu1) ... 125s Selecting previously unselected package libubsan1:arm64. 125s Preparing to unpack .../19-libubsan1_15.2.0-12ubuntu1_arm64.deb ... 125s Unpacking libubsan1:arm64 (15.2.0-12ubuntu1) ... 125s Selecting previously unselected package libhwasan0:arm64. 125s Preparing to unpack .../20-libhwasan0_15.2.0-12ubuntu1_arm64.deb ... 125s Unpacking libhwasan0:arm64 (15.2.0-12ubuntu1) ... 125s Selecting previously unselected package libgcc-15-dev:arm64. 125s Preparing to unpack .../21-libgcc-15-dev_15.2.0-12ubuntu1_arm64.deb ... 125s Unpacking libgcc-15-dev:arm64 (15.2.0-12ubuntu1) ... 125s Selecting previously unselected package gcc-15-aarch64-linux-gnu. 126s Preparing to unpack .../22-gcc-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 126s Unpacking gcc-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 126s Selecting previously unselected package gcc-15. 126s Preparing to unpack .../23-gcc-15_15.2.0-12ubuntu1_arm64.deb ... 126s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 126s Selecting previously unselected package gcc-aarch64-linux-gnu. 126s Preparing to unpack .../24-gcc-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 126s Unpacking gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 126s Selecting previously unselected package gcc. 126s Preparing to unpack .../25-gcc_4%3a15.2.0-4ubuntu1_arm64.deb ... 126s Unpacking gcc (4:15.2.0-4ubuntu1) ... 126s Selecting previously unselected package libstdc++-15-dev:arm64. 126s Preparing to unpack .../26-libstdc++-15-dev_15.2.0-12ubuntu1_arm64.deb ... 126s Unpacking libstdc++-15-dev:arm64 (15.2.0-12ubuntu1) ... 126s Selecting previously unselected package g++-15-aarch64-linux-gnu. 126s Preparing to unpack .../27-g++-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 126s Unpacking g++-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 126s Selecting previously unselected package g++-15. 127s Preparing to unpack .../28-g++-15_15.2.0-12ubuntu1_arm64.deb ... 127s Unpacking g++-15 (15.2.0-12ubuntu1) ... 127s Selecting previously unselected package g++-aarch64-linux-gnu. 127s Preparing to unpack .../29-g++-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 127s Unpacking g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 127s Selecting previously unselected package g++. 127s Preparing to unpack .../30-g++_4%3a15.2.0-4ubuntu1_arm64.deb ... 127s Unpacking g++ (4:15.2.0-4ubuntu1) ... 127s Selecting previously unselected package build-essential. 127s Preparing to unpack .../31-build-essential_12.12ubuntu2_arm64.deb ... 127s Unpacking build-essential (12.12ubuntu2) ... 127s Selecting previously unselected package runc. 127s Preparing to unpack .../32-runc_1.4.0-0ubuntu1_arm64.deb ... 127s Unpacking runc (1.4.0-0ubuntu1) ... 127s Selecting previously unselected package containerd. 127s Preparing to unpack .../33-containerd_2.2.1-0ubuntu1_arm64.deb ... 127s Unpacking containerd (2.2.1-0ubuntu1) ... 127s Selecting previously unselected package cwl-utils. 127s Preparing to unpack .../34-cwl-utils_0.40-1_all.deb ... 127s Unpacking cwl-utils (0.40-1) ... 127s Selecting previously unselected package python3-defusedxml. 127s Preparing to unpack .../35-python3-defusedxml_0.7.1-3build1_all.deb ... 127s Unpacking python3-defusedxml (0.7.1-3build1) ... 127s Selecting previously unselected package python3-junit.xml. 127s Preparing to unpack .../36-python3-junit.xml_1.9-6_all.deb ... 127s Unpacking python3-junit.xml (1.9-6) ... 127s Selecting previously unselected package python3-iniconfig. 127s Preparing to unpack .../37-python3-iniconfig_2.1.0-2_all.deb ... 127s Unpacking python3-iniconfig (2.1.0-2) ... 128s Selecting previously unselected package python3-pluggy. 128s Preparing to unpack .../38-python3-pluggy_1.6.0-2_all.deb ... 128s Unpacking python3-pluggy (1.6.0-2) ... 128s Selecting previously unselected package python3-pytest. 128s Preparing to unpack .../39-python3-pytest_9.0.2-2_all.deb ... 128s Unpacking python3-pytest (9.0.2-2) ... 128s Selecting previously unselected package cwltest. 128s Preparing to unpack .../40-cwltest_2.6.20251216093331-1_all.deb ... 128s Unpacking cwltest (2.6.20251216093331-1) ... 128s Selecting previously unselected package libjs-jquery. 128s Preparing to unpack .../41-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 128s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 128s Selecting previously unselected package fonts-font-awesome. 128s Preparing to unpack .../42-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1build1_all.deb ... 128s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 128s Selecting previously unselected package sphinx-rtd-theme-common. 128s Preparing to unpack .../43-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 128s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 128s Selecting previously unselected package cwltool-doc. 128s Preparing to unpack .../44-cwltool-doc_3.1.20251031082601-1_all.deb ... 128s Unpacking cwltool-doc (3.1.20251031082601-1) ... 128s Selecting previously unselected package libdebhelper-perl. 128s Preparing to unpack .../45-libdebhelper-perl_13.28ubuntu1_all.deb ... 128s Unpacking libdebhelper-perl (13.28ubuntu1) ... 128s Selecting previously unselected package libtool. 128s Preparing to unpack .../46-libtool_2.5.4-9_all.deb ... 128s Unpacking libtool (2.5.4-9) ... 128s Selecting previously unselected package dh-autoreconf. 128s Preparing to unpack .../47-dh-autoreconf_21_all.deb ... 128s Unpacking dh-autoreconf (21) ... 128s Selecting previously unselected package libarchive-zip-perl. 128s Preparing to unpack .../48-libarchive-zip-perl_1.68-1_all.deb ... 128s Unpacking libarchive-zip-perl (1.68-1) ... 128s Selecting previously unselected package libfile-stripnondeterminism-perl. 128s Preparing to unpack .../49-libfile-stripnondeterminism-perl_1.15.0-1build1_all.deb ... 128s Unpacking libfile-stripnondeterminism-perl (1.15.0-1build1) ... 128s Selecting previously unselected package dh-strip-nondeterminism. 128s Preparing to unpack .../50-dh-strip-nondeterminism_1.15.0-1build1_all.deb ... 128s Unpacking dh-strip-nondeterminism (1.15.0-1build1) ... 128s Selecting previously unselected package debugedit. 128s Preparing to unpack .../51-debugedit_1%3a5.2-3_arm64.deb ... 128s Unpacking debugedit (1:5.2-3) ... 128s Selecting previously unselected package dwz. 128s Preparing to unpack .../52-dwz_0.16-2_arm64.deb ... 128s Unpacking dwz (0.16-2) ... 128s Selecting previously unselected package gettext. 128s Preparing to unpack .../53-gettext_0.23.2-1_arm64.deb ... 128s Unpacking gettext (0.23.2-1) ... 128s Selecting previously unselected package intltool-debian. 128s Preparing to unpack .../54-intltool-debian_0.35.0+20060710.6build1_all.deb ... 128s Unpacking intltool-debian (0.35.0+20060710.6build1) ... 128s Selecting previously unselected package po-debconf. 128s Preparing to unpack .../55-po-debconf_1.0.22_all.deb ... 128s Unpacking po-debconf (1.0.22) ... 128s Selecting previously unselected package debhelper. 128s Preparing to unpack .../56-debhelper_13.28ubuntu1_all.deb ... 128s Unpacking debhelper (13.28ubuntu1) ... 128s Selecting previously unselected package dh-python. 129s Preparing to unpack .../57-dh-python_7.20260125_all.deb ... 129s Unpacking dh-python (7.20260125) ... 129s Selecting previously unselected package docker.io. 129s Preparing to unpack .../58-docker.io_29.1.3-0ubuntu1_arm64.deb ... 129s Unpacking docker.io (29.1.3-0ubuntu1) ... 129s Selecting previously unselected package sgml-base. 129s Preparing to unpack .../59-sgml-base_1.31+nmu1_all.deb ... 129s Unpacking sgml-base (1.31+nmu1) ... 129s Selecting previously unselected package xml-core. 129s Preparing to unpack .../60-xml-core_0.19build1_all.deb ... 129s Unpacking xml-core (0.19build1) ... 129s Selecting previously unselected package docutils-common. 129s Preparing to unpack .../61-docutils-common_0.22.4+dfsg-1_all.deb ... 129s Unpacking docutils-common (0.22.4+dfsg-1) ... 129s Selecting previously unselected package libjs-underscore. 129s Preparing to unpack .../62-libjs-underscore_1.13.7~dfsg+~1.13.0-1_all.deb ... 129s Unpacking libjs-underscore (1.13.7~dfsg+~1.13.0-1) ... 129s Selecting previously unselected package libjson-perl. 129s Preparing to unpack .../63-libjson-perl_4.10000-1_all.deb ... 129s Unpacking libjson-perl (4.10000-1) ... 129s Selecting previously unselected package libpython3.14-stdlib:arm64. 129s Preparing to unpack .../64-libpython3.14-stdlib_3.14.2-1_arm64.deb ... 129s Unpacking libpython3.14-stdlib:arm64 (3.14.2-1) ... 130s Selecting previously unselected package pybuild-plugin-autopkgtest. 130s Preparing to unpack .../65-pybuild-plugin-autopkgtest_7.20260125_all.deb ... 130s Unpacking pybuild-plugin-autopkgtest (7.20260125) ... 130s Selecting previously unselected package python3-pyproject-hooks. 130s Preparing to unpack .../66-python3-pyproject-hooks_1.2.0-1_all.deb ... 130s Unpacking python3-pyproject-hooks (1.2.0-1) ... 130s Selecting previously unselected package python3-wheel. 130s Preparing to unpack .../67-python3-wheel_0.46.1-2_all.deb ... 130s Unpacking python3-wheel (0.46.1-2) ... 130s Selecting previously unselected package python3-build. 130s Preparing to unpack .../68-python3-build_1.2.2-5_all.deb ... 130s Unpacking python3-build (1.2.2-5) ... 130s Selecting previously unselected package python3-installer. 130s Preparing to unpack .../69-python3-installer_0.7.0+dfsg1-3_all.deb ... 130s Unpacking python3-installer (0.7.0+dfsg1-3) ... 130s Selecting previously unselected package pybuild-plugin-pyproject. 130s Preparing to unpack .../70-pybuild-plugin-pyproject_7.20260125_all.deb ... 130s Unpacking pybuild-plugin-pyproject (7.20260125) ... 130s Selecting previously unselected package python3.14. 130s Preparing to unpack .../71-python3.14_3.14.2-1_arm64.deb ... 130s Unpacking python3.14 (3.14.2-1) ... 130s Selecting previously unselected package python3-all. 130s Preparing to unpack .../72-python3-all_3.13.9-3_arm64.deb ... 130s Unpacking python3-all (3.13.9-3) ... 130s Selecting previously unselected package python3-antlr4. 130s Preparing to unpack .../73-python3-antlr4_4.9.2-1build1_all.deb ... 130s Unpacking python3-antlr4 (4.9.2-1build1) ... 130s Selecting previously unselected package python3-astroid. 130s Preparing to unpack .../74-python3-astroid_4.0.2-1ubuntu1_all.deb ... 130s Unpacking python3-astroid (4.0.2-1ubuntu1) ... 130s Selecting previously unselected package python3.13-doc. 130s Preparing to unpack .../75-python3.13-doc_3.13.11-1_all.deb ... 130s Unpacking python3.13-doc (3.13.11-1) ... 130s Selecting previously unselected package python3-doc. 130s Preparing to unpack .../76-python3-doc_3.13.9-3_all.deb ... 130s Unpacking python3-doc (3.13.9-3) ... 130s Selecting previously unselected package python3-roman-numerals. 130s Preparing to unpack .../77-python3-roman-numerals_4.1.0-1_all.deb ... 130s Unpacking python3-roman-numerals (4.1.0-1) ... 130s Selecting previously unselected package python3-docutils. 130s Preparing to unpack .../78-python3-docutils_0.22.4+dfsg-1_all.deb ... 130s Unpacking python3-docutils (0.22.4+dfsg-1) ... 130s Selecting previously unselected package python3-execnet. 131s Preparing to unpack .../79-python3-execnet_2.1.1-1build1_all.deb ... 131s Unpacking python3-execnet (2.1.1-1build1) ... 131s Selecting previously unselected package python3-imagesize. 131s Preparing to unpack .../80-python3-imagesize_1.4.1-1build1_all.deb ... 131s Unpacking python3-imagesize (1.4.1-1build1) ... 131s Selecting previously unselected package python3-werkzeug. 131s Preparing to unpack .../81-python3-werkzeug_3.1.5-1_all.deb ... 131s Unpacking python3-werkzeug (3.1.5-1) ... 131s Selecting previously unselected package python3-pytest-httpserver. 131s Preparing to unpack .../82-python3-pytest-httpserver_1.1.3-1_all.deb ... 131s Unpacking python3-pytest-httpserver (1.1.3-1) ... 131s Selecting previously unselected package python3-pytest-timeout. 131s Preparing to unpack .../83-python3-pytest-timeout_2.4.0-2_all.deb ... 131s Unpacking python3-pytest-timeout (2.4.0-2) ... 131s Selecting previously unselected package python3-pytest-xdist. 131s Preparing to unpack .../84-python3-pytest-xdist_3.8.0-4_all.deb ... 131s Unpacking python3-pytest-xdist (3.8.0-4) ... 131s Selecting previously unselected package python3-pytz. 131s Preparing to unpack .../85-python3-pytz_2025.2-5_all.deb ... 131s Unpacking python3-pytz (2025.2-5) ... 131s Selecting previously unselected package python3-setuptools-scm. 131s Preparing to unpack .../86-python3-setuptools-scm_8.2.1-4_all.deb ... 131s Unpacking python3-setuptools-scm (8.2.1-4) ... 131s Selecting previously unselected package python3-snowballstemmer. 131s Preparing to unpack .../87-python3-snowballstemmer_3.0.1-1_all.deb ... 131s Unpacking python3-snowballstemmer (3.0.1-1) ... 131s Selecting previously unselected package sphinx-common. 131s Preparing to unpack .../88-sphinx-common_8.2.3-12_all.deb ... 131s Unpacking sphinx-common (8.2.3-12) ... 131s Selecting previously unselected package python3-alabaster. 131s Preparing to unpack .../89-python3-alabaster_0.7.16-0.1build1_all.deb ... 131s Unpacking python3-alabaster (0.7.16-0.1build1) ... 131s Selecting previously unselected package python3-sphinx. 131s Preparing to unpack .../90-python3-sphinx_8.2.3-12_all.deb ... 131s Unpacking python3-sphinx (8.2.3-12) ... 131s Selecting previously unselected package python3-sphinx-autoapi. 131s Preparing to unpack .../91-python3-sphinx-autoapi_3.6.1-1_all.deb ... 131s Unpacking python3-sphinx-autoapi (3.6.1-1) ... 131s Selecting previously unselected package python3-sphinx-autodoc-typehints. 131s Preparing to unpack .../92-python3-sphinx-autodoc-typehints_3.5.2-1_all.deb ... 131s Unpacking python3-sphinx-autodoc-typehints (3.5.2-1) ... 131s Selecting previously unselected package python3-sphinxcontrib.autoprogram. 131s Preparing to unpack .../93-python3-sphinxcontrib.autoprogram_0.1.9-1_all.deb ... 131s Unpacking python3-sphinxcontrib.autoprogram (0.1.9-1) ... 131s Selecting previously unselected package python3-stubserver. 131s Preparing to unpack .../94-python3-stubserver_1.1-4build1_all.deb ... 131s Unpacking python3-stubserver (1.1-4build1) ... 131s Selecting previously unselected package python3-tz. 131s Preparing to unpack .../95-python3-tz_2025.2-5_all.deb ... 131s Unpacking python3-tz (2025.2-5) ... 131s Selecting previously unselected package python3-wdlparse. 131s Preparing to unpack .../96-python3-wdlparse_0.1.0-3build1_all.deb ... 131s Unpacking python3-wdlparse (0.1.0-3build1) ... 131s Setting up dh-python (7.20260125) ... 132s Setting up python3-iniconfig (2.1.0-2) ... 132s Setting up python3-antlr4 (4.9.2-1build1) ... 132s Setting up gettext (0.23.2-1) ... 132s Setting up fonts-lato (2.015-1build1) ... 132s Setting up python3-defusedxml (0.7.1-3build1) ... 132s Setting up libarchive-zip-perl (1.68-1) ... 132s Setting up python3-alabaster (0.7.16-0.1build1) ... 133s Setting up python3-junit.xml (1.9-6) ... 133s Setting up libdebhelper-perl (13.28ubuntu1) ... 133s Setting up libpython3.14-minimal:arm64 (3.14.2-1) ... 133s Setting up m4 (1.4.20-2) ... 133s Setting up python3-pytz (2025.2-5) ... 133s Setting up python3-wheel (0.46.1-2) ... 133s Setting up python3-setuptools-scm (8.2.1-4) ... 133s Setting up python3-tz (2025.2-5) ... 133s Setting up runc (1.4.0-0ubuntu1) ... 133s Setting up intltool-debian (0.35.0+20060710.6build1) ... 133s Setting up python3-stubserver (1.1-4build1) ... 133s Setting up autotools-dev (20240727.1) ... 133s Setting up python3-pyproject-hooks (1.2.0-1) ... 134s Setting up python3-snowballstemmer (3.0.1-1) ... 134s Setting up python3-werkzeug (3.1.5-1) ... 134s Setting up cwl-utils (0.40-1) ... 134s Setting up libmpc3:arm64 (1.3.1-2) ... 134s Setting up autopoint (0.23.2-1) ... 134s Setting up python3-installer (0.7.0+dfsg1-3) ... 135s Setting up autoconf (2.72-3.1ubuntu1) ... 135s Setting up python3-pluggy (1.6.0-2) ... 135s Setting up libubsan1:arm64 (15.2.0-12ubuntu1) ... 135s Setting up dwz (0.16-2) ... 135s Setting up python3-astroid (4.0.2-1ubuntu1) ... 135s Setting up libhwasan0:arm64 (15.2.0-12ubuntu1) ... 135s Setting up libasan8:arm64 (15.2.0-12ubuntu1) ... 135s Setting up libjson-perl (4.10000-1) ... 135s Setting up python3-pytest-httpserver (1.1.3-1) ... 135s Setting up debugedit (1:5.2-3) ... 135s Setting up python3-roman-numerals (4.1.0-1) ... 136s Setting up sgml-base (1.31+nmu1) ... 136s Setting up libtsan2:arm64 (15.2.0-12ubuntu1) ... 136s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 136s Setting up libisl23:arm64 (0.27-1build1) ... 136s Setting up python3-build (1.2.2-5) ... 136s Setting up containerd (2.2.1-0ubuntu1) ... 136s Created symlink '/etc/systemd/system/multi-user.target.wants/containerd.service' → '/usr/lib/systemd/system/containerd.service'. 137s Setting up python3-execnet (2.1.1-1build1) ... 137s Setting up python3-wdlparse (0.1.0-3build1) ... 137s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 137s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 137s Setting up python3.14-minimal (3.14.2-1) ... 138s Setting up libcc1-0:arm64 (15.2.0-12ubuntu1) ... 138s Setting up liblsan0:arm64 (15.2.0-12ubuntu1) ... 138s Setting up libitm1:arm64 (15.2.0-12ubuntu1) ... 138s Setting up libjs-underscore (1.13.7~dfsg+~1.13.0-1) ... 138s Setting up python3-imagesize (1.4.1-1build1) ... 138s Setting up automake (1:1.18.1-3build1) ... 138s update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode 138s Setting up libfile-stripnondeterminism-perl (1.15.0-1build1) ... 138s Setting up cpp-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 138s Setting up cwltool-doc (3.1.20251031082601-1) ... 138s Setting up libgcc-15-dev:arm64 (15.2.0-12ubuntu1) ... 138s Setting up libpython3.14-stdlib:arm64 (3.14.2-1) ... 138s Setting up pybuild-plugin-pyproject (7.20260125) ... 138s Setting up python3-pytest (9.0.2-2) ... 139s Setting up po-debconf (1.0.22) ... 139s Setting up docker.io (29.1.3-0ubuntu1) ... 139s Created symlink '/etc/systemd/system/multi-user.target.wants/docker.service' → '/usr/lib/systemd/system/docker.service'. 139s Created symlink '/etc/systemd/system/sockets.target.wants/docker.socket' → '/usr/lib/systemd/system/docker.socket'. 140s Setting up python3.13-doc (3.13.11-1) ... 140s Setting up cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 140s Setting up libstdc++-15-dev:arm64 (15.2.0-12ubuntu1) ... 140s Setting up sphinx-common (8.2.3-12) ... 140s Setting up cwltest (2.6.20251216093331-1) ... 140s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 140s Setting up cpp-15 (15.2.0-12ubuntu1) ... 140s Setting up cpp (4:15.2.0-4ubuntu1) ... 140s Setting up xml-core (0.19build1) ... 140s Setting up python3.14 (3.14.2-1) ... 142s Setting up python3-doc (3.13.9-3) ... 142s Setting up gcc-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 142s Setting up python3-pytest-xdist (3.8.0-4) ... 142s Setting up python3-pytest-timeout (2.4.0-2) ... 142s Setting up python3-all (3.13.9-3) ... 142s Setting up gcc-15 (15.2.0-12ubuntu1) ... 142s Setting up g++-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 142s Setting up g++-15 (15.2.0-12ubuntu1) ... 142s Setting up gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 142s Setting up libtool (2.5.4-9) ... 142s Setting up gcc (4:15.2.0-4ubuntu1) ... 142s Setting up dh-autoreconf (21) ... 142s Setting up g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 142s Setting up debhelper (13.28ubuntu1) ... 142s Setting up g++ (4:15.2.0-4ubuntu1) ... 142s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 142s Setting up build-essential (12.12ubuntu2) ... 142s Setting up pybuild-plugin-autopkgtest (7.20260125) ... 142s Processing triggers for install-info (7.2-5) ... 142s Processing triggers for fontconfig (2.17.1-3ubuntu1) ... 142s Processing triggers for libc-bin (2.42-2ubuntu4) ... 142s Processing triggers for systemd (259-1ubuntu2) ... 142s Processing triggers for man-db (2.13.1-1) ... 144s Processing triggers for sgml-base (1.31+nmu1) ... 144s Setting up docutils-common (0.22.4+dfsg-1) ... 144s Processing triggers for sgml-base (1.31+nmu1) ... 144s Setting up python3-docutils (0.22.4+dfsg-1) ... 144s Setting up python3-sphinx (8.2.3-12) ... 146s Setting up python3-sphinx-autodoc-typehints (3.5.2-1) ... 146s Setting up python3-sphinx-autoapi (3.6.1-1) ... 146s Setting up python3-sphinxcontrib.autoprogram (0.1.9-1) ... 147s autopkgtest [05:40:23]: test pybuild-autopkgtest: pybuild-autopkgtest 147s autopkgtest [05:40:23]: test pybuild-autopkgtest: [----------------------- 149s pybuild-autopkgtest 149s I: pybuild base:384: cd /tmp/autopkgtest.leevCg/autopkgtest_tmp/build; python3.14 -m pytest -n 4 --dist loadscope -vv -W ignore -k "not (testVirtualEnv or DockstoreLookupTest or testMultiplejobs or testServices)" -m "not slow" --ignore /usr/lib/python3/dist-packages/toil/test/lib/aws/test_s3.py --ignore /usr/lib/python3/dist-packages/toil/test/provisioners/aws/awsProvisionerTest.py --ignore /usr/lib/python3/dist-packages/toil/test/wdl/wdltoil_test.py --ignore /usr/lib/python3/dist-packages/toil/test/cwl/cwlTest.py --ignore /usr/lib/python3/dist-packages/toil/test/lib/test_ec2.py --ignore /usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py --ignore /usr/lib/python3/dist-packages/toil/test/lib/aws/test_iam.py --ignore /usr/lib/python3/dist-packages/toil/test/provisioners/clusterTest.py --ignore /usr/lib/python3/dist-packages/toil/test/wdl/wdltoil_test_kubernetes.py --ignore /usr/lib/python3/dist-packages/toil/test/cactus/test_cactus_integration.py --pyargs toil.test 155s ============================= test session starts ============================== 155s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.14 155s cachedir: .pytest_cache 155s rootdir: /tmp/autopkgtest.leevCg/autopkgtest_tmp/build 155s configfile: setup.cfg 155s plugins: timeout-2.4.0, typeguard-4.4.4, cwltest-2.6.20251216093331, xdist-3.8.0, pytest_httpserver-1.1.3 155s created: 4/4 workers 155s 4 workers [375 items] 155s 155s scheduling tests via LoadScopeScheduling 155s 155s batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_default_gpu_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 155s jobStores/jobStoreTest.py::FileJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 0%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 0%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 0%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 1%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 1%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 1%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 1%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 2%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 2%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 2%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 2%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 3%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 3%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 3%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 4%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 4%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 4%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 4%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 5%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 5%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 5%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 5%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testMultiThreadImportFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 6%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testMultiThreadImportFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testOverlargeJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 6%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testOverlargeJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 6%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 6%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 7%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 7%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 7%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 8%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 8%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 8%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 8%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 9%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 9%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 9%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 9%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 10%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 10%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 10%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 10%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 11%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 11%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw1] [ 11%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 12%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw1] [ 12%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 12%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 12%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 13%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 13%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw1] [ 13%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw1] [ 13%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw1] [ 14%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 14%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw1] [ 14%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw1] [ 14%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 15%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw1] [ 15%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw1] [ 15%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 16%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 16%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw1] [ 16%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 16%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw1] [ 17%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s docs/scriptsTest.py::ToilDocumentationTest::testArguments <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 17%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 17%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 17%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 18%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 18%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 18%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 18%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 19%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s lib/dockerTest.py::TestDocker::testDockerClean <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 155s [gw3] [ 19%] PASSED batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_default_gpu_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 155s batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_get_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 155s [gw0] [ 19%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::FileJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw3] [ 20%] PASSED batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_get_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 155s batchSystems/test_slurm.py::SlurmTest::test_any_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 155s [gw0] [ 20%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::FileJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw3] [ 20%] PASSED batchSystems/test_slurm.py::SlurmTest::test_any_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 155s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 155s [gw0] [ 20%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw3] [ 21%] PASSED batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 155s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_mix_sacct_scontrol <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 155s [gw0] [ 21%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::FileJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw3] [ 21%] PASSED batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_mix_sacct_scontrol <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 155s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 155s [gw0] [ 21%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw3] [ 22%] PASSED batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 155s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 155s [gw0] [ 22%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s jobStores/jobStoreTest.py::FileJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw3] [ 22%] PASSED batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 155s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_sacct_raises_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 155s [gw3] [ 22%] PASSED batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_sacct_raises_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 155s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_sacct_raises_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 155s [gw3] [ 23%] PASSED batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_sacct_raises_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_some_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 23%] PASSED batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_some_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_argument_list_too_big <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 23%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_argument_list_too_big <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw0] [ 25%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 156s jobStores/jobStoreTest.py::FileJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 156s [gw3] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 27%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 27%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 27%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 28%] PASSED batchSystems/test_slurm.py::SlurmTest::test_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_export <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 28%] PASSED batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_export <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw3] [ 28%] PASSED batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_time <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw0] [ 28%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 157s jobStores/jobStoreTest.py::FileJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 157s [gw3] [ 29%] PASSED batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_time <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 158s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 158s [gw1] [ 29%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testArguments <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 159s docs/scriptsTest.py::ToilDocumentationTest::testDocker <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 159s [gw3] [ 29%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 160s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 160s [gw2] [ 29%] FAILED lib/dockerTest.py::TestDocker::testDockerClean <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 162s lib/dockerTest.py::TestDocker::testDockerClean_CRx_FORGO <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 164s [gw3] [ 30%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=True] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 164s [gw2] [ 30%] FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_FORGO <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 164s lib/dockerTest.py::TestDocker::testDockerClean_CRx_STOP <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 166s [gw3] [ 30%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 166s [gw1] [ 30%] FAILED docs/scriptsTest.py::ToilDocumentationTest::testDocker <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 167s docs/scriptsTest.py::ToilDocumentationTest::testDynamic <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 169s [gw3] [ 30%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 169s [gw2] [ 30%] FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_STOP <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 171s lib/dockerTest.py::TestDocker::testDockerClean_CRx_RM <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 175s [gw3] [ 30%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 175s [gw2] [ 31%] FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_RM <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 175s lib/dockerTest.py::TestDocker::testDockerPipeChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 179s [gw3] [ 31%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=True] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 182s [gw3] [ 31%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 182s [gw2] [ 31%] FAILED lib/dockerTest.py::TestDocker::testDockerPipeChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 182s lib/dockerTest.py::TestDocker::testDockerPipeChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 185s [gw3] [ 31%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 185s [gw3] [ 31%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 185s [gw3] [ 31%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 186s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 186s [gw0] [ 31%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 186s jobStores/jobStoreTest.py::FileJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 186s [gw0] [ 32%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 187s jobStores/jobStoreTest.py::FileJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 187s [gw2] [ 32%] FAILED lib/dockerTest.py::TestDocker::testDockerPipeChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 187s lib/dockerTest.py::TestDocker::testNonCachingDockerChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 187s [gw3] [ 32%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 189s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 189s [gw1] [ 32%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testDynamic <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 190s docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 190s [gw3] [ 33%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 192s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 192s [gw1] [ 33%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 193s docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 193s [gw3] [ 33%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 193s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 193s [gw2] [ 33%] FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 196s lib/dockerTest.py::TestDocker::testNonCachingDockerChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 196s [gw3] [ 34%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 199s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 199s [gw1] [ 34%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 200s docs/scriptsTest.py::ToilDocumentationTest::testHelloworld <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 200s [gw2] [ 34%] FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 205s lib/dockerTest.py::TestDocker::testDockerLogs <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 205s [gw1] [ 34%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testHelloworld <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 208s docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 208s [gw2] [ 35%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 208s lib/dockerTest.py::TestDocker::testDockerLogs_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 208s [gw1] [ 35%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 211s docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 211s [gw1] [ 35%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 214s docs/scriptsTest.py::ToilDocumentationTest::testJobFunctions <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 214s [gw2] [ 36%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 214s lib/dockerTest.py::TestDocker::testDockerLogs_Demux <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 214s [gw1] [ 36%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testJobFunctions <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 218s docs/scriptsTest.py::ToilDocumentationTest::testManaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 218s [gw1] [ 36%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testManaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 220s docs/scriptsTest.py::ToilDocumentationTest::testManaging2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 220s [gw2] [ 36%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 221s lib/dockerTest.py::TestDocker::testDockerLogs_Demux_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 221s [gw1] [ 37%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testManaging2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 224s docs/scriptsTest.py::ToilDocumentationTest::testPromises <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 224s [gw1] [ 37%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testPromises <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 225s docs/scriptsTest.py::ToilDocumentationTest::testPromises2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 225s [gw2] [ 37%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 225s src/dockerCheckTest.py::DockerCheckTest::testApplianceParser <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 225s [gw2] [ 37%] PASSED src/dockerCheckTest.py::DockerCheckTest::testApplianceParser <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 226s src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 226s [gw2] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 226s src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 226s [gw2] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 227s src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 227s [gw2] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 227s src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 227s [gw2] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 227s src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 227s [gw2] [ 39%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 227s src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 227s [gw2] [ 39%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 227s src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 227s [gw2] [ 39%] PASSED src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 227s src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 227s [gw2] [ 40%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 227s src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 227s [gw2] [ 40%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 227s src/dockerCheckTest.py::DockerCheckTest::testToilQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 227s [gw2] [ 40%] PASSED src/dockerCheckTest.py::DockerCheckTest::testToilQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 228s provisioners/clusterScalerTest.py::ClusterScalerTest::testBetaInertia <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s [gw2] [ 40%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testBetaInertia <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s provisioners/clusterScalerTest.py::ClusterScalerTest::testMaxNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s [gw2] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testMaxNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s provisioners/clusterScalerTest.py::ClusterScalerTest::testMinNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s [gw2] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testMinNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s provisioners/clusterScalerTest.py::ClusterScalerTest::testNoLaunchingIfDeltaAlreadyMet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s [gw2] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testNoLaunchingIfDeltaAlreadyMet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitIsSet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s [gw2] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitIsSet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitResponse <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s [gw2] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitResponse <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s provisioners/clusterScalerTest.py::ClusterScalerTest::testRounding <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s [gw2] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testRounding <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_large <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s [gw2] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_large <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_observed <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s [gw2] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_observed <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_small <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s [gw2] [ 43%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_small <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s server/serverTest.py::ToilWESServerWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 43%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 43%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 47%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 47%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 47%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s [gw2] [ 51%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 228s provisioners/clusterScalerTest.py::BinPackingTest::testAddingInitialNode <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s [gw2] [ 51%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testAddingInitialNode <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s provisioners/clusterScalerTest.py::BinPackingTest::testHighTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s [gw2] [ 51%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testHighTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s provisioners/clusterScalerTest.py::BinPackingTest::testJobTooLargeForAllNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 228s [gw2] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testJobTooLargeForAllNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 229s provisioners/clusterScalerTest.py::BinPackingTest::testLongRunningJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 229s [gw2] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testLongRunningJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 229s provisioners/clusterScalerTest.py::BinPackingTest::testLowTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 229s [gw2] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testLowTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 229s provisioners/clusterScalerTest.py::BinPackingTest::testPackingOneShape <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 229s [gw2] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testPackingOneShape <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 229s provisioners/clusterScalerTest.py::BinPackingTest::testPathologicalCase <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 229s [gw2] [ 53%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testPathologicalCase <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 229s provisioners/clusterScalerTest.py::BinPackingTest::testSorting <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 229s [gw2] [ 53%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testSorting <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 229s provisioners/clusterScalerTest.py::BinPackingTest::testZeroResourceJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 229s [gw2] [ 53%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testZeroResourceJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 229s utils/utilsTest.py::TestUtils::test_config_functionality <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 229s [gw2] [ 53%] PASSED utils/utilsTest.py::TestUtils::test_config_functionality <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 244s utils/utilsTest.py::TestUtils::testUtilsSort <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 244s [gw0] [ 54%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 244s jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 244s [gw0] [ 54%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 244s jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 244s [gw0] [ 54%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 244s jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 244s [gw0] [ 54%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 244s jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 244s [gw0] [ 55%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 244s jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 244s [gw0] [ 55%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 244s jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 244s [gw0] [ 55%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 244s jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 244s [gw0] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s [gw0] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s [gw0] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s [gw0] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s [gw0] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s [gw0] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s jobStores/jobStoreTest.py::FileJobStoreTest::test_file_link_imports <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s [gw0] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_file_link_imports <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_does_not_leak_symlinks <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s [gw0] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_does_not_leak_symlinks <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_init_preserves_symlink_path <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s [gw0] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_init_preserves_symlink_path <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s jobStores/jobStoreTest.py::FileJobStoreTest::test_symlink_read_control <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s [gw0] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_symlink_read_control <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 245s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 245s [gw0] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 245s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 245s [gw0] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s [gw0] [ 59%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s [gw0] [ 59%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s [gw0] [ 59%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s [gw0] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s [gw0] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s [gw0] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s [gw0] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s [gw0] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s [gw0] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s [gw0] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s [gw0] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 246s src/miscTests.py::TestMisc::testIDStability <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 246s [gw0] [ 62%] PASSED src/miscTests.py::TestMisc::testIDStability <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 246s src/miscTests.py::TestMisc::test_atomic_install <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 246s [gw0] [ 62%] PASSED src/miscTests.py::TestMisc::test_atomic_install <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 246s src/miscTests.py::TestMisc::test_atomic_install_dev <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 246s [gw0] [ 62%] PASSED src/miscTests.py::TestMisc::test_atomic_install_dev <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 246s src/miscTests.py::TestMisc::test_atomic_context_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 246s [gw0] [ 62%] PASSED src/miscTests.py::TestMisc::test_atomic_context_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 246s src/miscTests.py::TestMisc::test_atomic_context_error <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 246s [gw0] [ 63%] PASSED src/miscTests.py::TestMisc::test_atomic_context_error <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 246s src/miscTests.py::TestMisc::test_call_command_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 246s [gw0] [ 63%] PASSED src/miscTests.py::TestMisc::test_call_command_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 246s src/miscTests.py::TestMisc::test_call_command_err <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 246s [gw0] [ 63%] PASSED src/miscTests.py::TestMisc::test_call_command_err <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 246s lib/test_url.py::TestURLAccess::test_get_url_access <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 246s [gw0] [ 64%] PASSED lib/test_url.py::TestURLAccess::test_get_url_access <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 246s lib/test_url.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 246s [gw0] [ 64%] SKIPPED lib/test_url.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 246s lib/test_url.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 246s [gw0] [ 64%] SKIPPED lib/test_url.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 246s lib/test_url.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 246s [gw0] [ 64%] SKIPPED lib/test_url.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 246s lib/test_url.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 246s [gw0] [ 65%] SKIPPED lib/test_url.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 246s lib/test_url.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 246s [gw0] [ 65%] SKIPPED lib/test_url.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 246s lib/url_plugin_test.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 246s [gw0] [ 65%] PASSED lib/url_plugin_test.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 246s lib/url_plugin_test.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 246s [gw0] [ 65%] PASSED lib/url_plugin_test.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 246s lib/url_plugin_test.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 246s [gw0] [ 66%] PASSED lib/url_plugin_test.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 246s lib/url_plugin_test.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 246s [gw0] [ 66%] PASSED lib/url_plugin_test.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 246s lib/url_plugin_test.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 246s [gw0] [ 66%] PASSED lib/url_plugin_test.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 246s lib/url_plugin_test.py::TestURLAccess::test_url_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 246s [gw0] [ 66%] PASSED lib/url_plugin_test.py::TestURLAccess::test_url_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 250s src/retainTempDirTest.py::TestCleanWorkDir::testNever <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 250s [gw0] [ 67%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testNever <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 253s src/retainTempDirTest.py::TestCleanWorkDir::testAlways <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 253s [gw0] [ 67%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testAlways <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 255s src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 255s [gw1] [ 67%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testPromises2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 258s docs/scriptsTest.py::ToilDocumentationTest::testQuickstart <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 258s [gw1] [ 68%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testQuickstart <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 258s docs/scriptsTest.py::ToilDocumentationTest::testRequirements <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 258s [gw0] [ 68%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 261s src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithNoError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 261s [gw0] [ 68%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithNoError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 267s src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 267s [gw0] [ 68%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 267s src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithSuccess <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 267s [gw1] [ 69%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testRequirements <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 269s docs/scriptsTest.py::ToilDocumentationTest::testStaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 269s [gw0] [ 69%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithSuccess <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 269s lib/aws/test_utils.py::TagGenerationTest::test_build_tag <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 269s [gw0] [ 69%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_build_tag <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 269s lib/aws/test_utils.py::TagGenerationTest::test_build_tag_with_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 269s [gw0] [ 69%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_build_tag_with_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 269s lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 269s [gw0] [ 70%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 269s lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 269s [gw0] [ 70%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 269s lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 269s [gw0] [ 70%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 269s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s [gw0] [ 70%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s [gw0] [ 71%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s [gw0] [ 71%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s [gw0] [ 71%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s [gw0] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s [gw0] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s [gw0] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s [gw0] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s [gw0] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s [gw0] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 269s src/resourceTest.py::TestResource::testStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 269s [gw0] [ 73%] PASSED src/resourceTest.py::TestResource::testStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 269s src/resourceTest.py::TestResource::testPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 269s [gw0] [ 73%] PASSED src/resourceTest.py::TestResource::testPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 269s src/resourceTest.py::TestResource::testStandAloneInPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 269s [gw0] [ 74%] PASSED src/resourceTest.py::TestResource::testStandAloneInPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 270s src/resourceTest.py::TestResource::testBuiltIn <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 270s [gw0] [ 74%] PASSED src/resourceTest.py::TestResource::testBuiltIn <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 270s src/resourceTest.py::TestResource::testNonPyStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 270s [gw1] [ 74%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testStaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 272s docs/scriptsTest.py::ToilDocumentationTest::testStats <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 272s [gw0] [ 74%] PASSED src/resourceTest.py::TestResource::testNonPyStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 276s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 276s [gw0] [ 75%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 280s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithClassMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 280s [gw0] [ 75%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithClassMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 284s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithLambda <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 284s [gw0] [ 75%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithLambda <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 288s src/deferredFunctionTest.py::TestDeferredFunction::testBatchSystemCleanupCanHandleWorkerDeaths <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 288s [gw0] [ 76%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testBatchSystemCleanupCanHandleWorkerDeaths <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 288s src/miscTests.py::TestPanic::test_panic_by_hand <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 288s [gw0] [ 76%] PASSED src/miscTests.py::TestPanic::test_panic_by_hand <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 288s src/miscTests.py::TestPanic::test_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 288s [gw0] [ 76%] PASSED src/miscTests.py::TestPanic::test_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 288s src/miscTests.py::TestPanic::test_panic_with_secondary <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 288s [gw0] [ 76%] PASSED src/miscTests.py::TestPanic::test_panic_with_secondary <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 288s src/miscTests.py::TestPanic::test_nested_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 288s [gw0] [ 77%] PASSED src/miscTests.py::TestPanic::test_nested_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 288s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 288s [gw0] [ 77%] PASSED batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 288s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 288s [gw0] [ 77%] PASSED batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 288s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_still_running <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 288s [gw0] [ 77%] PASSED batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_still_running <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 288s lib/test_conversions.py::ConversionTest::test_convert <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 288s [gw0] [ 78%] PASSED lib/test_conversions.py::ConversionTest::test_convert <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 288s lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 288s [gw0] [ 78%] PASSED lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 288s lib/test_conversions.py::ConversionTest::test_human2bytes <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 288s [gw0] [ 78%] PASSED lib/test_conversions.py::ConversionTest::test_human2bytes <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 288s lib/test_history.py::TestHistory::test_history_submittable_detection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 288s [gw0] [ 78%] PASSED lib/test_history.py::TestHistory::test_history_submittable_detection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 288s lib/test_history.py::TestHistory::test_history_deletion <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 288s [gw0] [ 79%] PASSED lib/test_history.py::TestHistory::test_history_deletion <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 289s lib/test_history.py::TestHistory::test_history_size_limit <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 289s [gw0] [ 79%] PASSED lib/test_history.py::TestHistory::test_history_size_limit <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 289s server/serverTest.py::ToilWESServerBenchTest::test_get_service_info <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 289s [gw0] [ 79%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_get_service_info <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 289s server/serverTest.py::ToilWESServerBenchTest::test_health <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 289s [gw0] [ 80%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_health <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 289s server/serverTest.py::ToilWESServerBenchTest::test_home <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 289s [gw0] [ 80%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_home <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 289s src/busTest.py::TestMessageBus::test_enum_ints_in_file <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 289s [gw0] [ 80%] PASSED src/busTest.py::TestMessageBus::test_enum_ints_in_file <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 289s src/busTest.py::TestMessageBus::test_cross_thread_messaging <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 289s [gw0] [ 80%] PASSED src/busTest.py::TestMessageBus::test_cross_thread_messaging <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 296s src/busTest.py::TestMessageBus::test_restart_without_bus_path <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 296s [gw1] [ 81%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testStats <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 299s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 299s [gw0] [ 81%] PASSED src/busTest.py::TestMessageBus::test_restart_without_bus_path <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 299s src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 301s [gw1] [ 81%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 301s [gw0] [ 81%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 302s src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 306s [gw1] [ 81%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 308s [gw1] [ 81%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 311s [gw1] [ 81%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 311s [gw0] [ 82%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 311s src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 313s [gw1] [ 82%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 313s [gw0] [ 82%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 314s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 316s [gw1] [ 82%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 319s [gw1] [ 82%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 319s [gw1] [ 82%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 319s [gw1] [ 82%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 321s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 321s [gw1] [ 82%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 322s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 322s [gw0] [ 82%] PASSED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 330s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 330s [gw2] [ 83%] PASSED utils/utilsTest.py::TestUtils::testUtilsSort <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 330s utils/utilsTest.py::TestUtils::testUnicodeSupport <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 330s [gw1] [ 83%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 331s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 331s [gw0] [ 83%] FAILED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 332s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 332s [gw2] [ 84%] PASSED utils/utilsTest.py::TestUtils::testUnicodeSupport <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 335s utils/utilsTest.py::TestUtils::testGetPIDStatus <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 335s [gw1] [ 84%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 338s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 338s [gw1] [ 84%] SUBPASSED[Testing readwrite file permissions 338s [executable: True] 338s [caching: True] 338s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 338s [gw2] [ 84%] PASSED utils/utilsTest.py::TestUtils::testGetPIDStatus <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 340s utils/utilsTest.py::TestUtils::testGetStatusFailedToilWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 340s [gw0] [ 85%] FAILED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 340s src/promisedRequirementTest.py::TestMesosPromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 340s [gw0] [ 85%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 340s src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 340s [gw0] [ 85%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 340s src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 340s [gw0] [ 85%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 341s utils/toilDebugTest.py::TestDebugJob::test_run_job <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 341s [gw1] [ 85%] SUBPASSED[Testing readwrite file permissions 341s [executable: True] 341s [caching: False] 343s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 343s [gw1] [ 85%] SUBPASSED[Testing readwrite file permissions 343s [executable: False] 343s [caching: True] 344s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 344s [gw2] [ 86%] PASSED utils/utilsTest.py::TestUtils::testGetStatusFailedToilWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 346s utils/utilsTest.py::TestUtils::testGetStatusFailedCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 346s [gw1] [ 86%] SUBPASSED[Testing readwrite file permissions 346s [executable: False] 346s [caching: False] 346s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 346s [gw1] [ 86%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 347s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 347s [gw0] [ 86%] PASSED utils/toilDebugTest.py::TestDebugJob::test_run_job <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 348s utils/toilDebugTest.py::TestDebugJob::test_print_job_info <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 348s [gw1] [ 86%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 350s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 350s [gw2] [ 86%] PASSED utils/utilsTest.py::TestUtils::testGetStatusFailedCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 353s utils/utilsTest.py::TestUtils::testGetStatusSuccessfulCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 353s [gw1] [ 87%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 354s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 354s [gw0] [ 87%] PASSED utils/toilDebugTest.py::TestDebugJob::test_print_job_info <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 354s utils/toilDebugTest.py::TestDebugJob::test_retrieve_task_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 354s [gw0] [ 87%] SKIPPED utils/toilDebugTest.py::TestDebugJob::test_retrieve_task_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 354s __init__.py::toil.test.make_tests <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 354s [gw0] [ 88%] PASSED __init__.py::toil.test.make_tests <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 355s __init__.py::toil.test.timeLimit <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 355s [gw1] [ 88%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 355s options/options.py::OptionsTest::test_caching_option_priority <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 355s [gw2] [ 88%] PASSED utils/utilsTest.py::TestUtils::testGetStatusSuccessfulCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 355s utils/utilsTest.py::TestUtils::testPrintJobLog <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 355s [gw1] [ 88%] PASSED options/options.py::OptionsTest::test_caching_option_priority <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 355s options/options.py::OptionsTest::test_default_caching_slurm <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 355s [gw1] [ 89%] PASSED options/options.py::OptionsTest::test_default_caching_slurm <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 356s src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 356s [gw1] [ 89%] PASSED src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 356s src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 356s [gw0] [ 89%] PASSED __init__.py::toil.test.timeLimit <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 356s server/serverTest.py::AWSStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 356s [gw0] [ 89%] SKIPPED server/serverTest.py::AWSStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 356s server/serverTest.py::AWSStateStoreTest::test_state_store_paths <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 356s [gw0] [ 90%] SKIPPED server/serverTest.py::AWSStateStoreTest::test_state_store_paths <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 356s jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 356s [gw0] [ 90%] SKIPPED jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 356s lib/test_misc.py::UserNameAvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 356s [gw0] [ 90%] PASSED lib/test_misc.py::UserNameAvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 356s lib/test_misc.py::UserNameUnvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 356s [gw1] [ 90%] PASSED src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 356s batchSystems/batch_system_plugin_test.py::BatchSystemPluginTest::test_batchsystem_plugin_installable <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batch_system_plugin_test.py 356s [gw0] [ 91%] PASSED lib/test_misc.py::UserNameUnvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 356s lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 356s [gw0] [ 91%] PASSED lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 356s mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue <- ../../../../usr/lib/python3/dist-packages/toil/test/mesos/MesosDataStructuresTest.py 356s [gw0] [ 91%] PASSED mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue <- ../../../../usr/lib/python3/dist-packages/toil/test/mesos/MesosDataStructuresTest.py 356s server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 356s [gw0] [ 92%] SKIPPED server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 356s server/serverTest.py::FileStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 356s [gw0] [ 92%] SKIPPED server/serverTest.py::FileStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 356s server/serverTest.py::FileStateStoreURLTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 356s [gw0] [ 92%] SKIPPED server/serverTest.py::FileStateStoreURLTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 356s src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried <- ../../../../usr/lib/python3/dist-packages/toil/test/src/checkpointTest.py 356s [gw1] [ 92%] PASSED batchSystems/batch_system_plugin_test.py::BatchSystemPluginTest::test_batchsystem_plugin_installable <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batch_system_plugin_test.py 356s batchSystems/test_lsf_helper.py::LSFHelperTest::test_parse_mem_and_cmd_from_output <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_lsf_helper.py 356s [gw1] [ 93%] PASSED batchSystems/test_lsf_helper.py::LSFHelperTest::test_parse_mem_and_cmd_from_output <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_lsf_helper.py 356s provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/provisionerTest.py 356s [gw1] [ 93%] PASSED provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/provisionerTest.py 362s src/jobServiceTest.py::TestJobService::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 362s [gw2] [ 93%] PASSED utils/utilsTest.py::TestUtils::testPrintJobLog <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 363s utils/utilsTest.py::TestUtils::testRestartAttribute <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 363s [gw0] [ 93%] PASSED src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried <- ../../../../usr/lib/python3/dist-packages/toil/test/src/checkpointTest.py 380s src/environmentTest.py::EnvironmentTest::test_environment <- ../../../../usr/lib/python3/dist-packages/toil/test/src/environmentTest.py 380s [gw0] [ 94%] PASSED src/environmentTest.py::EnvironmentTest::test_environment <- ../../../../usr/lib/python3/dist-packages/toil/test/src/environmentTest.py 382s src/helloWorldTest.py::HelloWorldTest::testHelloWorld <- ../../../../usr/lib/python3/dist-packages/toil/test/src/helloWorldTest.py 382s [gw1] [ 94%] PASSED src/jobServiceTest.py::TestJobService::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 386s src/jobServiceTest.py::TestPerfectServicet::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 386s [gw2] [ 94%] PASSED utils/utilsTest.py::TestUtils::testRestartAttribute <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 387s src/threadingTest.py::TestThreading::testGlobalMutexOrdering <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 387s [gw0] [ 94%] PASSED src/helloWorldTest.py::HelloWorldTest::testHelloWorld <- ../../../../usr/lib/python3/dist-packages/toil/test/src/helloWorldTest.py 390s src/promisesTest.py::ChainedIndexedPromisesTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 390s [gw0] [ 95%] PASSED src/promisesTest.py::ChainedIndexedPromisesTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 394s src/promisesTest.py::PathIndexingPromiseTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 394s [gw0] [ 95%] PASSED src/promisesTest.py::PathIndexingPromiseTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 410s src/systemTest.py::TestSystem::testAtomicityOfNonEmptyDirectoryRenames <- ../../../../usr/lib/python3/dist-packages/toil/test/src/systemTest.py 410s [gw1] [ 95%] PASSED src/jobServiceTest.py::TestPerfectServicet::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 420s src/promisesTest.py::CachedUnpicklingJobStoreTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 420s [gw1] [ 96%] PASSED src/promisesTest.py::CachedUnpicklingJobStoreTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 421s src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger <- ../../../../usr/lib/python3/dist-packages/toil/test/src/realtimeLoggerTest.py 421s [gw2] [ 96%] PASSED src/threadingTest.py::TestThreading::testGlobalMutexOrdering <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 424s src/threadingTest.py::TestThreading::testLastProcessStanding <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 424s [gw1] [ 96%] PASSED src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger <- ../../../../usr/lib/python3/dist-packages/toil/test/src/realtimeLoggerTest.py 424s utils/toilKillTest.py::TestToilKill::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 424s [gw1] [ 96%] SKIPPED utils/toilKillTest.py::TestToilKill::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 424s utils/toilKillTest.py::TestToilKillWithAWSJobStore::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 450s [gw1] [ 97%] SKIPPED utils/toilKillTest.py::TestToilKillWithAWSJobStore::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 450s [gw3] [ 97%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 464s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 464s [gw3] [ 97%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 464s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 464s [gw2] [ 97%] PASSED src/threadingTest.py::TestThreading::testLastProcessStanding <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 475s src/resumabilityTest.py::TestResumability::test_chaining <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resumabilityTest.py 475s [gw3] [ 98%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 475s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 476s [gw2] [ 98%] PASSED src/resumabilityTest.py::TestResumability::test_chaining <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resumabilityTest.py 476s [gw3] [ 98%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 480s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 480s [gw3] [ 98%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 484s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 484s [gw3] [ 99%] SUBPASSED[Testing readwrite file permissions 484s [executable: True] 484s [caching: True] 488s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 488s [gw3] [ 99%] SUBPASSED[Testing readwrite file permissions 488s [executable: True] 488s [caching: False] 492s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 492s [gw3] [ 99%] SUBPASSED[Testing readwrite file permissions 492s [executable: False] 492s [caching: True] 496s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 496s [gw3] [ 99%] SUBPASSED[Testing readwrite file permissions 496s [executable: False] 496s [caching: False] 496s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 610s [gw3] [ 99%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 610s [gw0] [ 99%] PASSED src/systemTest.py::TestSystem::testAtomicityOfNonEmptyDirectoryRenames <- ../../../../usr/lib/python3/dist-packages/toil/test/src/systemTest.py 610s src/workerTest.py::WorkerTests::testNextChainable <- ../../../../usr/lib/python3/dist-packages/toil/test/src/workerTest.py 610s [gw0] [ 99%] PASSED src/workerTest.py::WorkerTests::testNextChainable <- ../../../../usr/lib/python3/dist-packages/toil/test/src/workerTest.py 617s utils/toilDebugTest.py::testFetchJobStoreFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 618s [gw0] [100%] PASSED utils/toilDebugTest.py::testFetchJobStoreFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 618s 618s ==================================== ERRORS ==================================== 618s _________________ ERROR collecting src/importExportFileTest.py _________________ 618s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py'. 618s Hint: make sure your test modules/packages have valid Python names. 618s Traceback: 618s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 618s mod = import_path( 618s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 618s importlib.import_module(module_name) 618s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 618s return _bootstrap._gcd_import(name[level:], package, level) 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s :1398: in _gcd_import 618s ??? 618s :1371: in _find_and_load 618s ??? 618s :1342: in _find_and_load_unlocked 618s ??? 618s :938: in _load_unlocked 618s ??? 618s :759: in exec_module 618s ??? 618s :491: in _call_with_frames_removed 618s ??? 618s /usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py:30: in 618s from pytest_subtests import SubTests 618s E ModuleNotFoundError: No module named 'pytest_subtests' 618s _________________ ERROR collecting src/jobEncapsulationTest.py _________________ 618s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py'. 618s Hint: make sure your test modules/packages have valid Python names. 618s Traceback: 618s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 618s mod = import_path( 618s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 618s importlib.import_module(module_name) 618s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 618s return _bootstrap._gcd_import(name[level:], package, level) 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s :1398: in _gcd_import 618s ??? 618s :1371: in _find_and_load 618s ??? 618s :1342: in _find_and_load_unlocked 618s ??? 618s :938: in _load_unlocked 618s ??? 618s :759: in exec_module 618s ??? 618s :491: in _call_with_frames_removed 618s ??? 618s /usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py:17: in 618s from toil.test.src.jobTest import fn1Test 618s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 618s from pytest_subtests import SubTests 618s E ModuleNotFoundError: No module named 'pytest_subtests' 618s _______________________ ERROR collecting src/jobTest.py ________________________ 618s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobTest.py'. 618s Hint: make sure your test modules/packages have valid Python names. 618s Traceback: 618s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 618s mod = import_path( 618s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 618s importlib.import_module(module_name) 618s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 618s return _bootstrap._gcd_import(name[level:], package, level) 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s :1398: in _gcd_import 618s ??? 618s :1371: in _find_and_load 618s ??? 618s :1342: in _find_and_load_unlocked 618s ??? 618s :938: in _load_unlocked 618s ??? 618s :759: in exec_module 618s ??? 618s :491: in _call_with_frames_removed 618s ??? 618s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 618s from pytest_subtests import SubTests 618s E ModuleNotFoundError: No module named 'pytest_subtests' 618s =================================== FAILURES =================================== 618s __________________________ TestDocker.testDockerClean __________________________ 618s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 618s toil.start(A) 618s ~~~~~~~~~~^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 618s return self._runMainLoop(rootJobDescription) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 618s ).run() 618s ~~~^^ 618s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 618s raise FailedJobsException( 618s ...<3 lines>... 618s ) 618s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v3 618s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v3" follows: 618s =========> 618s [2026-01-30T05:40:32+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:32+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:32+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1 618s [2026-01-30T05:40:32+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1 618s [2026-01-30T05:40:32+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:32+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 618s apiDockerCall( 618s ~~~~~~~~~~~~~^ 618s job, 618s ^^^^ 618s ...<6 lines>... 618s privileged=True, 618s ^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:32+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 618s result: TResult | None = func() 618s ~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 618s lambda: runtest_hook(item=item, **kwds), 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 618s yield 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 618s return result.get_result() 618s ~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 618s raise exc.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 618s res = yield 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 618s item.runtest() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 618s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 618s result = testfunction(**testargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 618s file_stats = test_file.stat() 618s File "/usr/lib/python3.14/pathlib/__init__.py", line 655, in stat 618s return os.stat(self, follow_symlinks=follow_symlinks) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean0/working/test.txt' 618s ----------------------------- Captured stderr call ----------------------------- 618s [2026-01-30T05:40:31+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of f15d1180-7930-4c04-bdec-67d3790d1130 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean0/jobstore 618s [2026-01-30T05:40:31+0000] [MainThread] [I] [toil.lib.history] Workflow f15d1180-7930-4c04-bdec-67d3790d1130 is a run of 618s [2026-01-30T05:40:31+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:31+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 618s [2026-01-30T05:40:32+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s [2026-01-30T05:40:32+0000] [Thread-2 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerCleanFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean0/jobstore kind-_testDockerCleanFn/instance-p1awpxu2. 618s [2026-01-30T05:40:32+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1 618s Exit reason: None 618s [2026-01-30T05:40:32+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v2 618s [2026-01-30T05:40:32+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-p1awpxu2" follows: 618s =========> 618s [2026-01-30T05:40:32+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:32+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:32+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1 618s [2026-01-30T05:40:32+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1 618s [2026-01-30T05:40:32+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:32+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 618s apiDockerCall( 618s ~~~~~~~~~~~~~^ 618s job, 618s ^^^^ 618s ...<6 lines>... 618s privileged=True, 618s ^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:32+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s [2026-01-30T05:40:32+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v2 with ID kind-_testDockerCleanFn/instance-p1awpxu2 to 0 618s [2026-01-30T05:40:32+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 618s [2026-01-30T05:40:32+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v3 is completely failed 618s [2026-01-30T05:40:33+0000] [Thread-5 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:40:33: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v3 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil.lib.history] Workflow f15d1180-7930-4c04-bdec-67d3790d1130 stopped. Success: False 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean0/jobstore) 618s ------------------------------ Captured log call ------------------------------- 618s INFO  toil.lib.history:history.py:369 Recording workflow creation of f15d1180-7930-4c04-bdec-67d3790d1130 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean0/jobstore 618s INFO  toil.lib.history:history.py:399 Workflow f15d1180-7930-4c04-bdec-67d3790d1130 is a run of 618s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 618s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerCleanFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean0/jobstore kind-_testDockerCleanFn/instance-p1awpxu2. 618s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1 618s Exit reason: None 618s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v2 618s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-p1awpxu2" follows: 618s =========> 618s [2026-01-30T05:40:32+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:32+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:32+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1 618s [2026-01-30T05:40:32+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1 618s [2026-01-30T05:40:32+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:32+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 618s apiDockerCall( 618s ~~~~~~~~~~~~~^ 618s job, 618s ^^^^ 618s ...<6 lines>... 618s privileged=True, 618s ^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:32+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v2 with ID kind-_testDockerCleanFn/instance-p1awpxu2 to 0 618s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 618s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v3 is completely failed 618s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:40:33: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 618s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 618s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-p1awpxu2 v3 618s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 618s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 618s INFO  toil.lib.history:history.py:530 Workflow f15d1180-7930-4c04-bdec-67d3790d1130 stopped. Success: False 618s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean0/jobstore) 618s _____________________ TestDocker.testDockerClean_CRx_FORGO _____________________ 618s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 618s toil.start(A) 618s ~~~~~~~~~~^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 618s return self._runMainLoop(rootJobDescription) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 618s ).run() 618s ~~~^^ 618s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 618s raise FailedJobsException( 618s ...<3 lines>... 618s ) 618s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_FORGO0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v3 618s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v3" follows: 618s =========> 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1 618s [2026-01-30T05:40:37+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1 618s [2026-01-30T05:40:37+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1 used 1.04x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:37+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 618s apiDockerCall( 618s ~~~~~~~~~~~~~^ 618s job, 618s ^^^^ 618s ...<6 lines>... 618s privileged=True, 618s ^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:37+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 618s result: TResult | None = func() 618s ~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 618s lambda: runtest_hook(item=item, **kwds), 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 618s yield 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 618s return result.get_result() 618s ~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 618s raise exc.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 618s res = yield 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 618s item.runtest() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 618s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 618s result = testfunction(**testargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 133, in testDockerClean_CRx_FORGO 618s self.testDockerClean( 618s ~~~~~~~~~~~~~~~~~~~~^ 618s tmp_path, caching=False, detached=False, rm=True, deferParam=FORGO 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 618s file_stats = test_file.stat() 618s File "/usr/lib/python3.14/pathlib/__init__.py", line 655, in stat 618s return os.stat(self, follow_symlinks=follow_symlinks) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_FORGO0/working/test.txt' 618s ----------------------------- Captured stderr call ----------------------------- 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 7f16071a-a10e-4e40-9828-3d12f58f9239 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_FORGO0/jobstore 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil.lib.history] Workflow 7f16071a-a10e-4e40-9828-3d12f58f9239 is a run of 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s [2026-01-30T05:40:37+0000] [Thread-6 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerCleanFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_FORGO0/jobstore kind-_testDockerCleanFn/instance-1wdiucyq. 618s [2026-01-30T05:40:37+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1 618s Exit reason: None 618s [2026-01-30T05:40:37+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v2 618s [2026-01-30T05:40:37+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-1wdiucyq" follows: 618s =========> 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1 618s [2026-01-30T05:40:37+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1 618s [2026-01-30T05:40:37+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1 used 1.04x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:37+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 618s apiDockerCall( 618s ~~~~~~~~~~~~~^ 618s job, 618s ^^^^ 618s ...<6 lines>... 618s privileged=True, 618s ^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:37+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s [2026-01-30T05:40:37+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v2 with ID kind-_testDockerCleanFn/instance-1wdiucyq to 0 618s [2026-01-30T05:40:37+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 618s [2026-01-30T05:40:37+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v3 is completely failed 618s [2026-01-30T05:40:37+0000] [Thread-9 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:40:37: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1 used 1.04x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 618s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 618s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v3 618s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil.lib.history] Workflow 7f16071a-a10e-4e40-9828-3d12f58f9239 stopped. Success: False 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_FORGO0/jobstore) 618s ------------------------------ Captured log call ------------------------------- 618s INFO  toil.lib.history:history.py:369 Recording workflow creation of 7f16071a-a10e-4e40-9828-3d12f58f9239 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_FORGO0/jobstore 618s INFO  toil.lib.history:history.py:399 Workflow 7f16071a-a10e-4e40-9828-3d12f58f9239 is a run of 618s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 618s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerCleanFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_FORGO0/jobstore kind-_testDockerCleanFn/instance-1wdiucyq. 618s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1 618s Exit reason: None 618s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v2 618s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-1wdiucyq" follows: 618s =========> 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:36+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1 618s [2026-01-30T05:40:37+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1 618s [2026-01-30T05:40:37+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1 used 1.04x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:37+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 618s apiDockerCall( 618s ~~~~~~~~~~~~~^ 618s job, 618s ^^^^ 618s ...<6 lines>... 618s privileged=True, 618s ^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:37+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v2 with ID kind-_testDockerCleanFn/instance-1wdiucyq to 0 618s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 618s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v3 is completely failed 618s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:40:37: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v1 used 1.04x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 618s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 618s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-1wdiucyq v3 618s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 618s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 618s INFO  toil.lib.history:history.py:530 Workflow 7f16071a-a10e-4e40-9828-3d12f58f9239 stopped. Success: False 618s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_FORGO0/jobstore) 618s _______________________ ToilDocumentationTest.testDocker _______________________ 618s [gw1] linux -- Python 3.14.2 /usr/bin/python3.14 618s Traceback (most recent call last): 618s File "/usr/lib/python3.14/unittest/case.py", line 58, in testPartExecutor 618s yield 618s File "/usr/lib/python3.14/unittest/case.py", line 669, in run 618s self._callTestMethod(testMethod) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ 618s File "/usr/lib/python3.14/unittest/case.py", line 615, in _callTestMethod 618s result = method() 618s File "/usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py", line 161, in testDocker 618s self.checkExitCode("tutorial_docker.py") 618s ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py", line 50, in checkExitCode 618s raise RuntimeError(stderr) 618s RuntimeError: [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of f5d80754-bf08-4d77-8640-6a3bc2da12a5 in file:/tmp/tmp0vm7_i1ututorial_docker 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.lib.history] Workflow f5d80754-bf08-4d77-8640-6a3bc2da12a5 is a run of /usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s [2026-01-30T05:40:35+0000] [Thread-4 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:40:35: Job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v1 used 1.04x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:35+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmp0vm7_i1ututorial_docker kind-apiDockerCall/instance-9q8y1fwn. 618s [2026-01-30T05:40:35+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v1 618s Exit reason: None 618s [2026-01-30T05:40:35+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v2 618s [2026-01-30T05:40:35+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-9q8y1fwn" follows: 618s =========> 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v1 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v1) from description 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v1 618s [2026-01-30T05:40:35+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v1 used 1.04x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:35+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:35+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s [2026-01-30T05:40:35+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v2 with ID kind-apiDockerCall/instance-9q8y1fwn to 1 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s [2026-01-30T05:40:36+0000] [Thread-4 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:40:36: Job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:36+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmp0vm7_i1ututorial_docker kind-apiDockerCall/instance-9q8y1fwn. 618s [2026-01-30T05:40:36+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v3 618s Exit reason: None 618s [2026-01-30T05:40:36+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v5 618s [2026-01-30T05:40:36+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-9q8y1fwn" follows: 618s =========> 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4) from description 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4 618s [2026-01-30T05:40:35+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:35+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:35+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s [2026-01-30T05:40:36+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v5 with ID kind-apiDockerCall/instance-9q8y1fwn to 0 618s [2026-01-30T05:40:36+0000] [MainThread] [W] [toil.leader] Job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v6 is completely failed 618s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 618s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 618s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v6 618s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 618s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 618s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.lib.history] Workflow f5d80754-bf08-4d77-8640-6a3bc2da12a5 stopped. Success: False 618s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/tmp0vm7_i1ututorial_docker) 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py", line 20, in 618s toil.start(align) 618s ~~~~~~~~~~^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 618s return self._runMainLoop(rootJobDescription) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 618s ).run() 618s ~~~^^ 618s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 618s raise FailedJobsException( 618s ...<3 lines>... 618s ) 618s toil.exceptions.FailedJobsException: The job store '/tmp/tmp0vm7_i1ututorial_docker' contains 1 failed jobs: 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v6 618s Log from job "'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v6" follows: 618s =========> 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4 618s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4) from description 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4 618s [2026-01-30T05:40:35+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:35+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:35+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s 618s ---------------------------- Captured stdout setup ----------------------------- 618s 618s 618s [TEST] toil.test.docs.scriptsTest.ToilDocumentationTest:testDocker (Jan 29 2026 21:40:34:748745 PST) 618s 618s 618s _____________________ TestDocker.testDockerClean_CRx_STOP ______________________ 618s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 618s toil.start(A) 618s ~~~~~~~~~~^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 618s return self._runMainLoop(rootJobDescription) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 618s ).run() 618s ~~~^^ 618s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 618s raise FailedJobsException( 618s ...<3 lines>... 618s ) 618s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_STOP0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v3 618s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v3" follows: 618s =========> 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1 618s [2026-01-30T05:40:41+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:41+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 618s apiDockerCall( 618s ~~~~~~~~~~~~~^ 618s job, 618s ^^^^ 618s ...<6 lines>... 618s privileged=True, 618s ^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:41+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 618s result: TResult | None = func() 618s ~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 618s lambda: runtest_hook(item=item, **kwds), 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 618s yield 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 618s return result.get_result() 618s ~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 618s raise exc.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 618s res = yield 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 618s item.runtest() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 618s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 618s result = testfunction(**testargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 138, in testDockerClean_CRx_STOP 618s self.testDockerClean( 618s ~~~~~~~~~~~~~~~~~~~~^ 618s tmp_path, caching=False, detached=False, rm=True, deferParam=STOP 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 618s file_stats = test_file.stat() 618s File "/usr/lib/python3.14/pathlib/__init__.py", line 655, in stat 618s return os.stat(self, follow_symlinks=follow_symlinks) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_STOP0/working/test.txt' 618s ----------------------------- Captured stderr call ----------------------------- 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of d52dcb7d-2dbf-4b95-9fd2-286bda1e2d37 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_STOP0/jobstore 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil.lib.history] Workflow d52dcb7d-2dbf-4b95-9fd2-286bda1e2d37 is a run of 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s [2026-01-30T05:40:42+0000] [Thread-10 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerCleanFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_STOP0/jobstore kind-_testDockerCleanFn/instance-rrprliu_. 618s [2026-01-30T05:40:42+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1 618s Exit reason: None 618s [2026-01-30T05:40:42+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v2 618s [2026-01-30T05:40:42+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-rrprliu_" follows: 618s =========> 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1 618s [2026-01-30T05:40:41+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:41+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 618s apiDockerCall( 618s ~~~~~~~~~~~~~^ 618s job, 618s ^^^^ 618s ...<6 lines>... 618s privileged=True, 618s ^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:41+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s [2026-01-30T05:40:42+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v2 with ID kind-_testDockerCleanFn/instance-rrprliu_ to 0 618s [2026-01-30T05:40:42+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 618s [2026-01-30T05:40:42+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v3 is completely failed 618s [2026-01-30T05:40:42+0000] [Thread-13 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:40:42: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:45+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 618s [2026-01-30T05:40:45+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 618s [2026-01-30T05:40:45+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v3 618s [2026-01-30T05:40:45+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 618s [2026-01-30T05:40:45+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 618s [2026-01-30T05:40:45+0000] [MainThread] [I] [toil.lib.history] Workflow d52dcb7d-2dbf-4b95-9fd2-286bda1e2d37 stopped. Success: False 618s [2026-01-30T05:40:45+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_STOP0/jobstore) 618s ------------------------------ Captured log call ------------------------------- 618s INFO  toil.lib.history:history.py:369 Recording workflow creation of d52dcb7d-2dbf-4b95-9fd2-286bda1e2d37 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_STOP0/jobstore 618s INFO  toil.lib.history:history.py:399 Workflow d52dcb7d-2dbf-4b95-9fd2-286bda1e2d37 is a run of 618s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 618s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerCleanFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_STOP0/jobstore kind-_testDockerCleanFn/instance-rrprliu_. 618s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1 618s Exit reason: None 618s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v2 618s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-rrprliu_" follows: 618s =========> 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1 618s [2026-01-30T05:40:41+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1 618s [2026-01-30T05:40:41+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:41+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 618s apiDockerCall( 618s ~~~~~~~~~~~~~^ 618s job, 618s ^^^^ 618s ...<6 lines>... 618s privileged=True, 618s ^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:41+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v2 with ID kind-_testDockerCleanFn/instance-rrprliu_ to 0 618s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 618s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v3 is completely failed 618s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:40:42: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 618s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 618s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-rrprliu_ v3 618s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 618s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 618s INFO  toil.lib.history:history.py:530 Workflow d52dcb7d-2dbf-4b95-9fd2-286bda1e2d37 stopped. Success: False 618s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_STOP0/jobstore) 618s ______________________ TestDocker.testDockerClean_CRx_RM _______________________ 618s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 618s toil.start(A) 618s ~~~~~~~~~~^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 618s return self._runMainLoop(rootJobDescription) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 618s ).run() 618s ~~~^^ 618s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 618s raise FailedJobsException( 618s ...<3 lines>... 618s ) 618s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_RM0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v3 618s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v3" follows: 618s =========> 618s [2026-01-30T05:40:46+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:46+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:46+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v1 618s [2026-01-30T05:40:46+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v1 618s [2026-01-30T05:40:46+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 618s apiDockerCall( 618s ~~~~~~~~~~~~~^ 618s job, 618s ^^^^ 618s ...<6 lines>... 618s privileged=True, 618s ^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:46+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 618s result: TResult | None = func() 618s ~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 618s lambda: runtest_hook(item=item, **kwds), 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 618s yield 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 618s return result.get_result() 618s ~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 618s raise exc.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 618s res = yield 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 618s item.runtest() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 618s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 618s result = testfunction(**testargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 143, in testDockerClean_CRx_RM 618s self.testDockerClean( 618s ~~~~~~~~~~~~~~~~~~~~^ 618s tmp_path, caching=False, detached=False, rm=True, deferParam=RM 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 618s file_stats = test_file.stat() 618s File "/usr/lib/python3.14/pathlib/__init__.py", line 655, in stat 618s return os.stat(self, follow_symlinks=follow_symlinks) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_RM0/working/test.txt' 618s ----------------------------- Captured stderr call ----------------------------- 618s [2026-01-30T05:40:46+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 0c1e7729-a509-4267-a6c5-95f28aff8be5 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_RM0/jobstore 618s [2026-01-30T05:40:46+0000] [MainThread] [I] [toil.lib.history] Workflow 0c1e7729-a509-4267-a6c5-95f28aff8be5 is a run of 618s [2026-01-30T05:40:46+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:46+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 618s [2026-01-30T05:40:46+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s [2026-01-30T05:40:47+0000] [Thread-14 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerCleanFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_RM0/jobstore kind-_testDockerCleanFn/instance-tprnphb1. 618s [2026-01-30T05:40:47+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v1 618s Exit reason: None 618s [2026-01-30T05:40:47+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v2 618s [2026-01-30T05:40:47+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-tprnphb1" follows: 618s =========> 618s [2026-01-30T05:40:46+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:46+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:46+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v1 618s [2026-01-30T05:40:46+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v1 618s [2026-01-30T05:40:46+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 618s apiDockerCall( 618s ~~~~~~~~~~~~~^ 618s job, 618s ^^^^ 618s ...<6 lines>... 618s privileged=True, 618s ^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:46+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s [2026-01-30T05:40:47+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v2 with ID kind-_testDockerCleanFn/instance-tprnphb1 to 0 618s [2026-01-30T05:40:47+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 618s [2026-01-30T05:40:47+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v3 is completely failed 618s [2026-01-30T05:40:51+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 618s [2026-01-30T05:40:51+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 618s [2026-01-30T05:40:51+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v3 618s [2026-01-30T05:40:51+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 618s [2026-01-30T05:40:51+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 618s [2026-01-30T05:40:51+0000] [MainThread] [I] [toil.lib.history] Workflow 0c1e7729-a509-4267-a6c5-95f28aff8be5 stopped. Success: False 618s [2026-01-30T05:40:51+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_RM0/jobstore) 618s ------------------------------ Captured log call ------------------------------- 618s INFO  toil.lib.history:history.py:369 Recording workflow creation of 0c1e7729-a509-4267-a6c5-95f28aff8be5 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_RM0/jobstore 618s INFO  toil.lib.history:history.py:399 Workflow 0c1e7729-a509-4267-a6c5-95f28aff8be5 is a run of 618s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 618s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerCleanFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_RM0/jobstore kind-_testDockerCleanFn/instance-tprnphb1. 618s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v1 618s Exit reason: None 618s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v2 618s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-tprnphb1" follows: 618s =========> 618s [2026-01-30T05:40:46+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:46+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:46+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v1 618s [2026-01-30T05:40:46+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v1 618s [2026-01-30T05:40:46+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 618s apiDockerCall( 618s ~~~~~~~~~~~~~^ 618s job, 618s ^^^^ 618s ...<6 lines>... 618s privileged=True, 618s ^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:46+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v2 with ID kind-_testDockerCleanFn/instance-tprnphb1 to 0 618s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 618s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v3 is completely failed 618s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 618s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 618s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tprnphb1 v3 618s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 618s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 618s INFO  toil.lib.history:history.py:530 Workflow 0c1e7729-a509-4267-a6c5-95f28aff8be5 stopped. Success: False 618s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_RM0/jobstore) 618s ________________________ TestDocker.testDockerPipeChain ________________________ 618s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 618s result: TResult | None = func() 618s ~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 618s lambda: runtest_hook(item=item, **kwds), 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 618s yield 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 618s return result.get_result() 618s ~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 618s raise exc.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 618s res = yield 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 618s item.runtest() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 618s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 618s result = testfunction(**testargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 310, in testDockerPipeChain 618s rv = Job.Runner.startToil(A, options) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 618s return toil.start(job) 618s ~~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 618s return self._runMainLoop(rootJobDescription) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 618s ).run() 618s ~~~^^ 618s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 618s raise FailedJobsException( 618s ...<3 lines>... 618s ) 618s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v6 618s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v6" follows: 618s =========> 618s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4 618s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4 618s [2026-01-30T05:40:53+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:53+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 618s return apiDockerCall( 618s job, 618s ...<2 lines>... 618s privileged=True, 618s ) 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:53+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s ----------------------------- Captured stderr call ----------------------------- 618s [2026-01-30T05:40:51+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 868088f7-2f29-4e82-a3bd-1f74bc44fd57 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChain0/jobstore 618s [2026-01-30T05:40:51+0000] [MainThread] [I] [toil.lib.history] Workflow 868088f7-2f29-4e82-a3bd-1f74bc44fd57 is a run of 618s [2026-01-30T05:40:51+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:51+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 618s [2026-01-30T05:40:51+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s [2026-01-30T05:40:53+0000] [Thread-18 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-t4a93sh1. 618s [2026-01-30T05:40:53+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v1 618s Exit reason: None 618s [2026-01-30T05:40:53+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v2 618s [2026-01-30T05:40:53+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-t4a93sh1" follows: 618s =========> 618s [2026-01-30T05:40:52+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:52+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:52+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v1 618s [2026-01-30T05:40:52+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v1 618s [2026-01-30T05:40:52+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 618s return apiDockerCall( 618s job, 618s ...<2 lines>... 618s privileged=True, 618s ) 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:52+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s [2026-01-30T05:40:53+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v2 with ID kind-_testDockerPipeChainFn/instance-t4a93sh1 to 1 618s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 618s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s [2026-01-30T05:40:54+0000] [Thread-18 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-t4a93sh1. 618s [2026-01-30T05:40:54+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v3 618s Exit reason: None 618s [2026-01-30T05:40:54+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v5 618s [2026-01-30T05:40:54+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-t4a93sh1" follows: 618s =========> 618s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4 618s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4 618s [2026-01-30T05:40:53+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:53+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 618s return apiDockerCall( 618s job, 618s ...<2 lines>... 618s privileged=True, 618s ) 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:53+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s [2026-01-30T05:40:54+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v5 with ID kind-_testDockerPipeChainFn/instance-t4a93sh1 to 0 618s [2026-01-30T05:40:54+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v6 is completely failed 618s [2026-01-30T05:40:54+0000] [Thread-21 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:40:54: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:57+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 618s [2026-01-30T05:40:57+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 618s [2026-01-30T05:40:57+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v6 618s [2026-01-30T05:40:57+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 618s [2026-01-30T05:40:58+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 618s [2026-01-30T05:40:58+0000] [MainThread] [I] [toil.lib.history] Workflow 868088f7-2f29-4e82-a3bd-1f74bc44fd57 stopped. Success: False 618s [2026-01-30T05:40:58+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChain0/jobstore) 618s ------------------------------ Captured log call ------------------------------- 618s INFO  toil.lib.history:history.py:369 Recording workflow creation of 868088f7-2f29-4e82-a3bd-1f74bc44fd57 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChain0/jobstore 618s INFO  toil.lib.history:history.py:399 Workflow 868088f7-2f29-4e82-a3bd-1f74bc44fd57 is a run of 618s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 618s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-t4a93sh1. 618s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v1 618s Exit reason: None 618s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v2 618s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-t4a93sh1" follows: 618s =========> 618s [2026-01-30T05:40:52+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:52+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:52+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v1 618s [2026-01-30T05:40:52+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v1 618s [2026-01-30T05:40:52+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 618s return apiDockerCall( 618s job, 618s ...<2 lines>... 618s privileged=True, 618s ) 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:52+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v2 with ID kind-_testDockerPipeChainFn/instance-t4a93sh1 to 1 618s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 618s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-t4a93sh1. 618s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v3 618s Exit reason: None 618s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v5 618s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-t4a93sh1" follows: 618s =========> 618s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4 618s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4 618s [2026-01-30T05:40:53+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:53+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 618s return apiDockerCall( 618s job, 618s ...<2 lines>... 618s privileged=True, 618s ) 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:53+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v5 with ID kind-_testDockerPipeChainFn/instance-t4a93sh1 to 0 618s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v6 is completely failed 618s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:40:54: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 618s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 618s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v6 618s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 618s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 618s INFO  toil.lib.history:history.py:530 Workflow 868088f7-2f29-4e82-a3bd-1f74bc44fd57 stopped. Success: False 618s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChain0/jobstore) 618s _________________ TestDocker.testDockerPipeChainErrorDetection _________________ 618s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 618s result: TResult | None = func() 618s ~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 618s lambda: runtest_hook(item=item, **kwds), 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 618s yield 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 618s return result.get_result() 618s ~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 618s raise exc.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 618s res = yield 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 618s item.runtest() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 618s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 618s result = testfunction(**testargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 332, in testDockerPipeChainErrorDetection 618s rv = Job.Runner.startToil(A, options) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 618s return toil.start(job) 618s ~~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 618s return self._runMainLoop(rootJobDescription) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 618s ).run() 618s ~~~^^ 618s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 618s raise FailedJobsException( 618s ...<3 lines>... 618s ) 618s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChainErrorDetect0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v6 618s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v6" follows: 618s =========> 618s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4 618s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4 618s [2026-01-30T05:40:59+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:59+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 618s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 618s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:59+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s ----------------------------- Captured stderr call ----------------------------- 618s [2026-01-30T05:40:58+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 997097d6-8379-43ff-9b75-22b5dd19b547 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChainErrorDetect0/jobstore 618s [2026-01-30T05:40:58+0000] [MainThread] [I] [toil.lib.history] Workflow 997097d6-8379-43ff-9b75-22b5dd19b547 is a run of 618s [2026-01-30T05:40:58+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:58+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 618s [2026-01-30T05:40:58+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s [2026-01-30T05:40:59+0000] [Thread-22 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainErrorFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9. 618s [2026-01-30T05:40:59+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v1 618s Exit reason: None 618s [2026-01-30T05:40:59+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v2 618s [2026-01-30T05:40:59+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9" follows: 618s =========> 618s [2026-01-30T05:40:58+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:58+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:58+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v1 618s [2026-01-30T05:40:58+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v1 618s [2026-01-30T05:40:58+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v1 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:58+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 618s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 618s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:58+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s [2026-01-30T05:40:59+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v2 with ID kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 to 1 618s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 618s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s [2026-01-30T05:40:59+0000] [Thread-25 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:40:59: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v1 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:59+0000] [Thread-25 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:40:59: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:41:00+0000] [Thread-22 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainErrorFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9. 618s [2026-01-30T05:41:00+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v3 618s Exit reason: None 618s [2026-01-30T05:41:00+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v5 618s [2026-01-30T05:41:00+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9" follows: 618s =========> 618s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4 618s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4 618s [2026-01-30T05:40:59+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:59+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 618s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 618s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:59+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s [2026-01-30T05:41:00+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v5 with ID kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 to 0 618s [2026-01-30T05:41:00+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v6 is completely failed 618s [2026-01-30T05:41:03+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 618s [2026-01-30T05:41:03+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 618s [2026-01-30T05:41:03+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v6 618s [2026-01-30T05:41:03+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 618s [2026-01-30T05:41:03+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 618s [2026-01-30T05:41:04+0000] [MainThread] [I] [toil.lib.history] Workflow 997097d6-8379-43ff-9b75-22b5dd19b547 stopped. Success: False 618s [2026-01-30T05:41:04+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChainErrorDetect0/jobstore) 618s ------------------------------ Captured log call ------------------------------- 618s INFO  toil.lib.history:history.py:369 Recording workflow creation of 997097d6-8379-43ff-9b75-22b5dd19b547 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChainErrorDetect0/jobstore 618s INFO  toil.lib.history:history.py:399 Workflow 997097d6-8379-43ff-9b75-22b5dd19b547 is a run of 618s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 618s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainErrorFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9. 618s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v1 618s Exit reason: None 618s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v2 618s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9" follows: 618s =========> 618s [2026-01-30T05:40:58+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:58+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:58+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v1 618s [2026-01-30T05:40:58+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v1 618s [2026-01-30T05:40:58+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v1 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:58+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 618s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 618s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:58+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v2 with ID kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 to 1 618s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 618s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:40:59: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v1 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:40:59: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainErrorFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9. 618s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v3 618s Exit reason: None 618s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v5 618s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9" follows: 618s =========> 618s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4 618s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4 618s [2026-01-30T05:40:59+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:40:59+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 618s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 618s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:40:59+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v5 with ID kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 to 0 618s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v6 is completely failed 618s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 618s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 618s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v6 618s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 618s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 618s INFO  toil.lib.history:history.py:530 Workflow 997097d6-8379-43ff-9b75-22b5dd19b547 stopped. Success: False 618s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChainErrorDetect0/jobstore) 618s _____________________ TestDocker.testNonCachingDockerChain _____________________ 618s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 618s result: TResult | None = func() 618s ~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 618s lambda: runtest_hook(item=item, **kwds), 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 618s yield 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 618s return result.get_result() 618s ~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 618s raise exc.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 618s res = yield 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 618s item.runtest() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 618s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 618s result = testfunction(**testargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 336, in testNonCachingDockerChain 618s self.testDockerPipeChain(tmp_path, caching=True) 618s ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 310, in testDockerPipeChain 618s rv = Job.Runner.startToil(A, options) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 618s return toil.start(job) 618s ~~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 618s return self._runMainLoop(rootJobDescription) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 618s ).run() 618s ~~~^^ 618s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 618s raise FailedJobsException( 618s ...<3 lines>... 618s ) 618s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v6 618s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v6" follows: 618s =========> 618s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4 618s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4 618s [2026-01-30T05:41:05+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:41:05+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 618s return apiDockerCall( 618s job, 618s ...<2 lines>... 618s privileged=True, 618s ) 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:41:05+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s ----------------------------- Captured stderr call ----------------------------- 618s [2026-01-30T05:41:04+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of f0f295f0-e07b-4664-9a6b-d2ce3a47fe1a in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChain0/jobstore 618s [2026-01-30T05:41:04+0000] [MainThread] [I] [toil.lib.history] Workflow f0f295f0-e07b-4664-9a6b-d2ce3a47fe1a is a run of 618s [2026-01-30T05:41:04+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:41:04+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 618s [2026-01-30T05:41:04+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s [2026-01-30T05:41:05+0000] [Thread-26 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-su26s9av. 618s [2026-01-30T05:41:05+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v1 618s Exit reason: None 618s [2026-01-30T05:41:05+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v2 618s [2026-01-30T05:41:05+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-su26s9av" follows: 618s =========> 618s [2026-01-30T05:41:04+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:41:04+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:41:04+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v1 618s [2026-01-30T05:41:04+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v1 618s [2026-01-30T05:41:04+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v1 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:41:04+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 618s return apiDockerCall( 618s job, 618s ...<2 lines>... 618s privileged=True, 618s ) 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:41:04+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s [2026-01-30T05:41:05+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v2 with ID kind-_testDockerPipeChainFn/instance-su26s9av to 1 618s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 618s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s [2026-01-30T05:41:05+0000] [Thread-29 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:41:05: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v1 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:41:05+0000] [Thread-26 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-su26s9av. 618s [2026-01-30T05:41:05+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v3 618s Exit reason: None 618s [2026-01-30T05:41:05+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v5 618s [2026-01-30T05:41:05+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-su26s9av" follows: 618s =========> 618s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4 618s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4 618s [2026-01-30T05:41:05+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:41:05+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 618s return apiDockerCall( 618s job, 618s ...<2 lines>... 618s privileged=True, 618s ) 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:41:05+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s [2026-01-30T05:41:05+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v5 with ID kind-_testDockerPipeChainFn/instance-su26s9av to 0 618s [2026-01-30T05:41:05+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v6 is completely failed 618s [2026-01-30T05:41:06+0000] [Thread-29 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:41:06: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:41:09+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 618s [2026-01-30T05:41:09+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 618s [2026-01-30T05:41:09+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v6 618s [2026-01-30T05:41:09+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 618s [2026-01-30T05:41:09+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 618s [2026-01-30T05:41:09+0000] [MainThread] [I] [toil.lib.history] Workflow f0f295f0-e07b-4664-9a6b-d2ce3a47fe1a stopped. Success: False 618s [2026-01-30T05:41:09+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChain0/jobstore) 618s ------------------------------ Captured log call ------------------------------- 618s INFO  toil.lib.history:history.py:369 Recording workflow creation of f0f295f0-e07b-4664-9a6b-d2ce3a47fe1a in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChain0/jobstore 618s INFO  toil.lib.history:history.py:399 Workflow f0f295f0-e07b-4664-9a6b-d2ce3a47fe1a is a run of 618s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 618s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-su26s9av. 618s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v1 618s Exit reason: None 618s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v2 618s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-su26s9av" follows: 618s =========> 618s [2026-01-30T05:41:04+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:41:04+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:41:04+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v1 618s [2026-01-30T05:41:04+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v1 618s [2026-01-30T05:41:04+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v1 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:41:04+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 618s return apiDockerCall( 618s job, 618s ...<2 lines>... 618s privileged=True, 618s ) 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:41:04+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v2 with ID kind-_testDockerPipeChainFn/instance-su26s9av to 1 618s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 618s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:41:05: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v1 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-su26s9av. 618s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v3 618s Exit reason: None 618s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v5 618s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-su26s9av" follows: 618s =========> 618s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4 618s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4 618s [2026-01-30T05:41:05+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:41:05+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 618s return apiDockerCall( 618s job, 618s ...<2 lines>... 618s privileged=True, 618s ) 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:41:05+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v5 with ID kind-_testDockerPipeChainFn/instance-su26s9av to 0 618s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v6 is completely failed 618s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:41:06: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 618s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 618s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v6 618s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 618s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 618s INFO  toil.lib.history:history.py:530 Workflow f0f295f0-e07b-4664-9a6b-d2ce3a47fe1a stopped. Success: False 618s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChain0/jobstore) 618s ______________ TestDocker.testNonCachingDockerChainErrorDetection ______________ 618s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 618s result: TResult | None = func() 618s ~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 618s lambda: runtest_hook(item=item, **kwds), 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 618s yield 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 618s return result.get_result() 618s ~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 618s raise exc.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 618s res = yield 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 618s item.runtest() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 618s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 618s result = testfunction(**testargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 339, in testNonCachingDockerChainErrorDetection 618s self.testDockerPipeChainErrorDetection(tmp_path, caching=True) 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 332, in testDockerPipeChainErrorDetection 618s rv = Job.Runner.startToil(A, options) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 618s return toil.start(job) 618s ~~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 618s return self._runMainLoop(rootJobDescription) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 618s ).run() 618s ~~~^^ 618s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 618s raise FailedJobsException( 618s ...<3 lines>... 618s ) 618s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChainError0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v6 618s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v6" follows: 618s =========> 618s [2026-01-30T05:41:11+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:41:11+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:41:11+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4 618s [2026-01-30T05:41:11+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4 618s [2026-01-30T05:41:11+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:41:11+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 618s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 618s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:41:11+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s ----------------------------- Captured stderr call ----------------------------- 618s [2026-01-30T05:41:09+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of a0d79617-101a-4a38-a366-22a1375142f3 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChainError0/jobstore 618s [2026-01-30T05:41:09+0000] [MainThread] [I] [toil.lib.history] Workflow a0d79617-101a-4a38-a366-22a1375142f3 is a run of 618s [2026-01-30T05:41:09+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:41:09+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 618s [2026-01-30T05:41:09+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s [2026-01-30T05:41:10+0000] [Thread-33 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:41:10: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:41:10+0000] [Thread-30 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainErrorFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-4iyb6omh. 618s [2026-01-30T05:41:10+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v1 618s Exit reason: None 618s [2026-01-30T05:41:10+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v2 618s [2026-01-30T05:41:10+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-4iyb6omh" follows: 618s =========> 618s [2026-01-30T05:41:10+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:41:10+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:41:10+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v1 618s [2026-01-30T05:41:10+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v1 618s [2026-01-30T05:41:10+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:41:10+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 618s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 618s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:41:10+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s [2026-01-30T05:41:10+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v2 with ID kind-_testDockerPipeChainErrorFn/instance-4iyb6omh to 1 618s [2026-01-30T05:41:10+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 618s [2026-01-30T05:41:10+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s [2026-01-30T05:41:11+0000] [Thread-33 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:41:11: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:41:11+0000] [Thread-30 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainErrorFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-4iyb6omh. 618s [2026-01-30T05:41:11+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v3 618s Exit reason: None 618s [2026-01-30T05:41:11+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v5 618s [2026-01-30T05:41:11+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-4iyb6omh" follows: 618s =========> 618s [2026-01-30T05:41:11+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:41:11+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:41:11+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4 618s [2026-01-30T05:41:11+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4 618s [2026-01-30T05:41:11+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:41:11+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 618s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 618s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:41:11+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s [2026-01-30T05:41:11+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v5 with ID kind-_testDockerPipeChainErrorFn/instance-4iyb6omh to 0 618s [2026-01-30T05:41:11+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v6 is completely failed 618s [2026-01-30T05:41:16+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 618s [2026-01-30T05:41:16+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 618s [2026-01-30T05:41:16+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v6 618s [2026-01-30T05:41:16+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 618s [2026-01-30T05:41:16+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 618s [2026-01-30T05:41:16+0000] [MainThread] [I] [toil.lib.history] Workflow a0d79617-101a-4a38-a366-22a1375142f3 stopped. Success: False 618s [2026-01-30T05:41:16+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChainError0/jobstore) 618s ------------------------------ Captured log call ------------------------------- 618s INFO  toil.lib.history:history.py:369 Recording workflow creation of a0d79617-101a-4a38-a366-22a1375142f3 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChainError0/jobstore 618s INFO  toil.lib.history:history.py:399 Workflow a0d79617-101a-4a38-a366-22a1375142f3 is a run of 618s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 618s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:41:10: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainErrorFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-4iyb6omh. 618s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v1 618s Exit reason: None 618s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v2 618s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-4iyb6omh" follows: 618s =========> 618s [2026-01-30T05:41:10+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:41:10+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:41:10+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v1 618s [2026-01-30T05:41:10+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v1 618s [2026-01-30T05:41:10+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:41:10+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 618s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 618s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:41:10+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v2 with ID kind-_testDockerPipeChainErrorFn/instance-4iyb6omh to 1 618s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 618s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 618s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:41:11: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainErrorFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-4iyb6omh. 618s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v3 618s Exit reason: None 618s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v5 618s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-4iyb6omh" follows: 618s =========> 618s [2026-01-30T05:41:11+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:41:11+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:41:11+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4 618s [2026-01-30T05:41:11+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4 618s [2026-01-30T05:41:11+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:41:11+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 618s return self.version(api_version=False)["ApiVersion"] 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 618s return self._result(self._get(url), json=True) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 618s return f(self, *args, **kwargs) 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 618s return self.get(url, **self._set_request_timeout(kwargs)) 618s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 618s return self.request("GET", url, **kwargs) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 618s resp = self.send(prep, **send_kwargs) 618s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 618s r = adapter.send(request, **kwargs) 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 618s raise ConnectionError(err, request=request) 618s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s The above exception was the direct cause of the following exception: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 618s job._runner( 618s ~~~~~~~~~~~^ 618s jobGraph=None, 618s ^^^^^^^^^^^^^^ 618s ...<2 lines>... 618s defer=defer, 618s ^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 618s returnValues = self._run(jobGraph=None, fileStore=fileStore) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 618s return self.run(fileStore) 618s ~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 618s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 618s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 618s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 618s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 618s return cls( 618s timeout=timeout, 618s ...<3 lines>... 618s **kwargs_from_env(**kwargs) 618s ) 618s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 618s self.api = APIClient(*args, **kwargs) 618s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 618s self._version = self._retrieve_server_version() 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 618s raise DockerException( 618s f'Error while fetching server API version: {e}' 618s ) from e 618s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 618s 618s [2026-01-30T05:41:11+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 618s <========= 618s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v5 with ID kind-_testDockerPipeChainErrorFn/instance-4iyb6omh to 0 618s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v6 is completely failed 618s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 618s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 618s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v6 618s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 618s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 618s INFO  toil.lib.history:history.py:530 Workflow a0d79617-101a-4a38-a366-22a1375142f3 stopped. Success: False 618s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChainError0/jobstore) 618s __________________________ TestDocker.testDockerLogs ___________________________ 618s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 618s result: TResult | None = func() 618s ~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 618s lambda: runtest_hook(item=item, **kwds), 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 618s yield 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 618s return result.get_result() 618s ~~~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 618s raise exc.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 618s res = yield 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 618s teardown.throw(exception) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 618s return (yield) 618s ^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 618s item.runtest() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 618s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 618s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 618s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 618s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 618s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 618s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 618s raise exception 618s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 618s res = hook_impl.function(*args) 618s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 618s result = testfunction(**testargs) 618s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 618s rv = Job.Runner.startToil(A, options) 618s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 618s return toil.start(job) 618s ~~~~~~~~~~^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 618s return self._runMainLoop(rootJobDescription) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 618s ).run() 618s ~~~^^ 618s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 618s raise FailedJobsException( 618s ...<3 lines>... 618s ) 618s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v6 618s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v6" follows: 618s =========> 618s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 618s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 618s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4 618s [2026-01-30T05:41:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4 618s [2026-01-30T05:41:20+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 618s [2026-01-30T05:41:20+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 618s ...<10 lines>... 618s **response_kw, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 618s conn.request( 618s ~~~~~~~~~~~~^ 618s method, 618s ^^^^^^^ 618s ...<6 lines>... 618s enforce_content_length=enforce_content_length, 618s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s ) 618s ^ 618s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 618s self.endheaders() 618s ~~~~~~~~~~~~~~~^^ 618s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 618s self._send_output(message_body, encode_chunked=encode_chunked) 618s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 618s self.send(msg) 618s ~~~~~~~~~^^^^^ 618s File "/usr/lib/python3.13/http/client.py", line 1057, in send 618s self.connect() 618s ~~~~~~~~~~~~^^ 618s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 618s sock.connect(self.unix_socket) 618s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 618s PermissionError: [Errno 13] Permission denied 618s 618s During handling of the above exception, another exception occurred: 618s 618s Traceback (most recent call last): 618s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 618s resp = conn.urlopen( 618s method=request.method, 618s ...<9 lines>... 618s chunked=chunked, 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 618s retries = retries.increment( 618s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 618s ) 618s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 618s raise reraise(type(error), error, _stacktrace) 618s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 618s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 618s raise value.with_traceback(tb) 618s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 618s response = self._make_request( 618s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:20+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s ----------------------------- Captured stderr call ----------------------------- 619s [2026-01-30T05:41:17+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 91589fc5-3278-434c-9358-dede70b54318 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs0/jobstore 619s [2026-01-30T05:41:18+0000] [MainThread] [I] [toil.lib.history] Workflow 91589fc5-3278-434c-9358-dede70b54318 is a run of 619s [2026-01-30T05:41:18+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:18+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 619s [2026-01-30T05:41:18+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s [2026-01-30T05:41:19+0000] [Thread-34 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-sivp4v4f. 619s [2026-01-30T05:41:19+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v1 619s Exit reason: None 619s [2026-01-30T05:41:19+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v2 619s [2026-01-30T05:41:19+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-sivp4v4f" follows: 619s =========> 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v1 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v1 619s [2026-01-30T05:41:19+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:19+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s [2026-01-30T05:41:19+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v2 with ID kind-_testDockerLogsFn/instance-sivp4v4f to 1 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s [2026-01-30T05:41:20+0000] [Thread-34 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-sivp4v4f. 619s [2026-01-30T05:41:20+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v3 619s Exit reason: None 619s [2026-01-30T05:41:20+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v5 619s [2026-01-30T05:41:20+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-sivp4v4f" follows: 619s =========> 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4 619s [2026-01-30T05:41:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4 619s [2026-01-30T05:41:20+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:20+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:20+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s [2026-01-30T05:41:20+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v5 with ID kind-_testDockerLogsFn/instance-sivp4v4f to 0 619s [2026-01-30T05:41:20+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v6 is completely failed 619s [2026-01-30T05:41:20+0000] [Thread-37 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:41:20: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:24+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 619s [2026-01-30T05:41:24+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 619s [2026-01-30T05:41:24+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v6 619s [2026-01-30T05:41:24+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 619s [2026-01-30T05:41:25+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 619s [2026-01-30T05:41:25+0000] [MainThread] [I] [toil.lib.history] Workflow 91589fc5-3278-434c-9358-dede70b54318 stopped. Success: False 619s [2026-01-30T05:41:25+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs0/jobstore) 619s ------------------------------ Captured log call ------------------------------- 619s INFO  toil.lib.history:history.py:369 Recording workflow creation of 91589fc5-3278-434c-9358-dede70b54318 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs0/jobstore 619s INFO  toil.lib.history:history.py:399 Workflow 91589fc5-3278-434c-9358-dede70b54318 is a run of 619s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 619s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-sivp4v4f. 619s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v1 619s Exit reason: None 619s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v2 619s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-sivp4v4f" follows: 619s =========> 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v1 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v1 619s [2026-01-30T05:41:19+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:19+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v2 with ID kind-_testDockerLogsFn/instance-sivp4v4f to 1 619s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 619s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-sivp4v4f. 619s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v3 619s Exit reason: None 619s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v5 619s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-sivp4v4f" follows: 619s =========> 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4 619s [2026-01-30T05:41:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4 619s [2026-01-30T05:41:20+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:20+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:20+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v5 with ID kind-_testDockerLogsFn/instance-sivp4v4f to 0 619s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v6 is completely failed 619s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:41:20: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 619s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 619s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v6 619s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 619s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 619s INFO  toil.lib.history:history.py:530 Workflow 91589fc5-3278-434c-9358-dede70b54318 stopped. Success: False 619s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs0/jobstore) 619s _______________________ TestDocker.testDockerLogs_Stream _______________________ 619s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 619s result: TResult | None = func() 619s ~~~~^^ 619s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 619s lambda: runtest_hook(item=item, **kwds), 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 619s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 619s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 619s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 619s raise exception 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 619s yield 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 619s return (yield) 619s ^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 619s return result.get_result() 619s ~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 619s raise exc.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 619s res = yield 619s ^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 619s return (yield) 619s ^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 619s res = hook_impl.function(*args) 619s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 619s item.runtest() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 619s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 619s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 619s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 619s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 619s raise exception 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 619s res = hook_impl.function(*args) 619s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 619s result = testfunction(**testargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 366, in testDockerLogs_Stream 619s self.testDockerLogs(tmp_path, stream=True, demux=False) 619s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 619s rv = Job.Runner.startToil(A, options) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 619s return toil.start(job) 619s ~~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 619s return self._runMainLoop(rootJobDescription) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 619s ).run() 619s ~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 619s raise FailedJobsException( 619s ...<3 lines>... 619s ) 619s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v6 619s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v6" follows: 619s =========> 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4 619s [2026-01-30T05:41:26+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:26+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:26+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s ----------------------------- Captured stderr call ----------------------------- 619s [2026-01-30T05:41:25+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 74e65cb6-8491-4b20-a090-9050bdb21a8e in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Stream0/jobstore 619s [2026-01-30T05:41:25+0000] [MainThread] [I] [toil.lib.history] Workflow 74e65cb6-8491-4b20-a090-9050bdb21a8e is a run of 619s [2026-01-30T05:41:25+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:25+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 619s [2026-01-30T05:41:25+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s [2026-01-30T05:41:26+0000] [Thread-38 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-th744hzf. 619s [2026-01-30T05:41:26+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v1 619s Exit reason: None 619s [2026-01-30T05:41:26+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v2 619s [2026-01-30T05:41:26+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-th744hzf" follows: 619s =========> 619s [2026-01-30T05:41:25+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:25+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:25+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v1 619s [2026-01-30T05:41:25+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v1 619s [2026-01-30T05:41:25+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:25+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:25+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s [2026-01-30T05:41:26+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v2 with ID kind-_testDockerLogsFn/instance-th744hzf to 1 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s [2026-01-30T05:41:26+0000] [Thread-41 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:41:26: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:26+0000] [Thread-38 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-th744hzf. 619s [2026-01-30T05:41:26+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v3 619s Exit reason: None 619s [2026-01-30T05:41:26+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v5 619s [2026-01-30T05:41:26+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-th744hzf" follows: 619s =========> 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4 619s [2026-01-30T05:41:26+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:26+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:26+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s [2026-01-30T05:41:26+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v5 with ID kind-_testDockerLogsFn/instance-th744hzf to 0 619s [2026-01-30T05:41:26+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v6 is completely failed 619s [2026-01-30T05:41:27+0000] [Thread-41 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:41:27: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:30+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 619s [2026-01-30T05:41:30+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 619s [2026-01-30T05:41:30+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v6 619s [2026-01-30T05:41:30+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 619s [2026-01-30T05:41:30+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 619s [2026-01-30T05:41:30+0000] [MainThread] [I] [toil.lib.history] Workflow 74e65cb6-8491-4b20-a090-9050bdb21a8e stopped. Success: False 619s [2026-01-30T05:41:30+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Stream0/jobstore) 619s ------------------------------ Captured log call ------------------------------- 619s INFO  toil.lib.history:history.py:369 Recording workflow creation of 74e65cb6-8491-4b20-a090-9050bdb21a8e in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Stream0/jobstore 619s INFO  toil.lib.history:history.py:399 Workflow 74e65cb6-8491-4b20-a090-9050bdb21a8e is a run of 619s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 619s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-th744hzf. 619s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v1 619s Exit reason: None 619s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v2 619s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-th744hzf" follows: 619s =========> 619s [2026-01-30T05:41:25+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:25+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:25+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v1 619s [2026-01-30T05:41:25+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v1 619s [2026-01-30T05:41:25+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:25+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:25+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v2 with ID kind-_testDockerLogsFn/instance-th744hzf to 1 619s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 619s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:41:26: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-th744hzf. 619s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v3 619s Exit reason: None 619s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v5 619s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-th744hzf" follows: 619s =========> 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4 619s [2026-01-30T05:41:26+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:26+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:26+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v5 with ID kind-_testDockerLogsFn/instance-th744hzf to 0 619s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v6 is completely failed 619s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:41:27: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 619s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 619s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v6 619s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 619s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 619s INFO  toil.lib.history:history.py:530 Workflow 74e65cb6-8491-4b20-a090-9050bdb21a8e stopped. Success: False 619s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Stream0/jobstore) 619s _______________________ TestDocker.testDockerLogs_Demux ________________________ 619s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 619s result: TResult | None = func() 619s ~~~~^^ 619s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 619s lambda: runtest_hook(item=item, **kwds), 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 619s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 619s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 619s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 619s raise exception 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 619s yield 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 619s return (yield) 619s ^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 619s return result.get_result() 619s ~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 619s raise exc.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 619s res = yield 619s ^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 619s return (yield) 619s ^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 619s res = hook_impl.function(*args) 619s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 619s item.runtest() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 619s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 619s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 619s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 619s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 619s raise exception 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 619s res = hook_impl.function(*args) 619s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 619s result = testfunction(**testargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 369, in testDockerLogs_Demux 619s self.testDockerLogs(tmp_path, stream=False, demux=True) 619s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 619s rv = Job.Runner.startToil(A, options) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 619s return toil.start(job) 619s ~~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 619s return self._runMainLoop(rootJobDescription) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 619s ).run() 619s ~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 619s raise FailedJobsException( 619s ...<3 lines>... 619s ) 619s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v6 619s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v6" follows: 619s =========> 619s [2026-01-30T05:41:32+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:32+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:32+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4 619s [2026-01-30T05:41:32+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4 619s [2026-01-30T05:41:32+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:32+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:32+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s ----------------------------- Captured stderr call ----------------------------- 619s [2026-01-30T05:41:30+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of ac8782a3-8c0e-4769-b89d-c67f5c35d2f1 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux0/jobstore 619s [2026-01-30T05:41:30+0000] [MainThread] [I] [toil.lib.history] Workflow ac8782a3-8c0e-4769-b89d-c67f5c35d2f1 is a run of 619s [2026-01-30T05:41:30+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:30+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 619s [2026-01-30T05:41:30+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s [2026-01-30T05:41:31+0000] [Thread-42 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-aqx8erqz. 619s [2026-01-30T05:41:31+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v1 619s Exit reason: None 619s [2026-01-30T05:41:31+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v2 619s [2026-01-30T05:41:31+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-aqx8erqz" follows: 619s =========> 619s [2026-01-30T05:41:31+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:31+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:31+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v1 619s [2026-01-30T05:41:31+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v1 619s [2026-01-30T05:41:31+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:31+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:31+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s [2026-01-30T05:41:31+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v2 with ID kind-_testDockerLogsFn/instance-aqx8erqz to 1 619s [2026-01-30T05:41:31+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 619s [2026-01-30T05:41:31+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s [2026-01-30T05:41:31+0000] [Thread-45 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:41:31: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:32+0000] [Thread-42 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-aqx8erqz. 619s [2026-01-30T05:41:32+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v3 619s Exit reason: None 619s [2026-01-30T05:41:32+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v5 619s [2026-01-30T05:41:32+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-aqx8erqz" follows: 619s =========> 619s [2026-01-30T05:41:32+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:32+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:32+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4 619s [2026-01-30T05:41:32+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4 619s [2026-01-30T05:41:32+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:32+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:32+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s [2026-01-30T05:41:32+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v5 with ID kind-_testDockerLogsFn/instance-aqx8erqz to 0 619s [2026-01-30T05:41:32+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v6 is completely failed 619s [2026-01-30T05:41:32+0000] [Thread-45 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:41:32: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:35+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 619s [2026-01-30T05:41:35+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 619s [2026-01-30T05:41:35+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v6 619s [2026-01-30T05:41:35+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 619s [2026-01-30T05:41:36+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 619s [2026-01-30T05:41:36+0000] [MainThread] [I] [toil.lib.history] Workflow ac8782a3-8c0e-4769-b89d-c67f5c35d2f1 stopped. Success: False 619s [2026-01-30T05:41:36+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux0/jobstore) 619s ------------------------------ Captured log call ------------------------------- 619s INFO  toil.lib.history:history.py:369 Recording workflow creation of ac8782a3-8c0e-4769-b89d-c67f5c35d2f1 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux0/jobstore 619s INFO  toil.lib.history:history.py:399 Workflow ac8782a3-8c0e-4769-b89d-c67f5c35d2f1 is a run of 619s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 619s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-aqx8erqz. 619s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v1 619s Exit reason: None 619s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v2 619s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-aqx8erqz" follows: 619s =========> 619s [2026-01-30T05:41:31+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:31+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:31+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v1 619s [2026-01-30T05:41:31+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v1 619s [2026-01-30T05:41:31+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:31+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:31+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v2 with ID kind-_testDockerLogsFn/instance-aqx8erqz to 1 619s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 619s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:41:31: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-aqx8erqz. 619s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v3 619s Exit reason: None 619s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v5 619s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-aqx8erqz" follows: 619s =========> 619s [2026-01-30T05:41:32+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:32+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:32+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4 619s [2026-01-30T05:41:32+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4 619s [2026-01-30T05:41:32+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:32+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:32+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v5 with ID kind-_testDockerLogsFn/instance-aqx8erqz to 0 619s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v6 is completely failed 619s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:41:32: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 619s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 619s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v6 619s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 619s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 619s INFO  toil.lib.history:history.py:530 Workflow ac8782a3-8c0e-4769-b89d-c67f5c35d2f1 stopped. Success: False 619s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux0/jobstore) 619s ____________________ TestDocker.testDockerLogs_Demux_Stream ____________________ 619s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 619s result: TResult | None = func() 619s ~~~~^^ 619s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 619s lambda: runtest_hook(item=item, **kwds), 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 619s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 619s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 619s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 619s raise exception 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 619s yield 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 619s return (yield) 619s ^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 619s return result.get_result() 619s ~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 619s raise exc.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 619s res = yield 619s ^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 619s return (yield) 619s ^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 619s res = hook_impl.function(*args) 619s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 619s item.runtest() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 619s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 619s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 619s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 619s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 619s raise exception 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 619s res = hook_impl.function(*args) 619s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 619s result = testfunction(**testargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 372, in testDockerLogs_Demux_Stream 619s self.testDockerLogs(tmp_path, stream=True, demux=True) 619s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 619s rv = Job.Runner.startToil(A, options) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 619s return toil.start(job) 619s ~~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 619s return self._runMainLoop(rootJobDescription) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 619s ).run() 619s ~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 619s raise FailedJobsException( 619s ...<3 lines>... 619s ) 619s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v6 619s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v6" follows: 619s =========> 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4 619s [2026-01-30T05:41:37+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:37+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:37+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s ----------------------------- Captured stderr call ----------------------------- 619s [2026-01-30T05:41:36+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 7a5e7e64-2116-4e65-b211-ad046a85c63d in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux_Stream0/jobstore 619s [2026-01-30T05:41:36+0000] [MainThread] [I] [toil.lib.history] Workflow 7a5e7e64-2116-4e65-b211-ad046a85c63d is a run of 619s [2026-01-30T05:41:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:36+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 619s [2026-01-30T05:41:36+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s [2026-01-30T05:41:37+0000] [Thread-46 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-nrenh16w. 619s [2026-01-30T05:41:37+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v1 619s Exit reason: None 619s [2026-01-30T05:41:37+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v2 619s [2026-01-30T05:41:37+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-nrenh16w" follows: 619s =========> 619s [2026-01-30T05:41:36+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:36+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v1 619s [2026-01-30T05:41:36+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v1 619s [2026-01-30T05:41:36+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:36+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:36+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s [2026-01-30T05:41:37+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v2 with ID kind-_testDockerLogsFn/instance-nrenh16w to 1 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s [2026-01-30T05:41:37+0000] [Thread-49 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:41:37: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:38+0000] [Thread-46 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-nrenh16w. 619s [2026-01-30T05:41:38+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v3 619s Exit reason: None 619s [2026-01-30T05:41:38+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v5 619s [2026-01-30T05:41:38+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-nrenh16w" follows: 619s =========> 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4 619s [2026-01-30T05:41:37+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:37+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:37+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s [2026-01-30T05:41:38+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v5 with ID kind-_testDockerLogsFn/instance-nrenh16w to 0 619s [2026-01-30T05:41:38+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v6 is completely failed 619s [2026-01-30T05:41:38+0000] [Thread-49 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:41:38: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:41+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 619s [2026-01-30T05:41:41+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 619s [2026-01-30T05:41:41+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v6 619s [2026-01-30T05:41:41+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 619s [2026-01-30T05:41:41+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 619s [2026-01-30T05:41:41+0000] [MainThread] [I] [toil.lib.history] Workflow 7a5e7e64-2116-4e65-b211-ad046a85c63d stopped. Success: False 619s [2026-01-30T05:41:42+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux_Stream0/jobstore) 619s ------------------------------ Captured log call ------------------------------- 619s INFO  toil.lib.history:history.py:369 Recording workflow creation of 7a5e7e64-2116-4e65-b211-ad046a85c63d in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux_Stream0/jobstore 619s INFO  toil.lib.history:history.py:399 Workflow 7a5e7e64-2116-4e65-b211-ad046a85c63d is a run of 619s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 619s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-nrenh16w. 619s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v1 619s Exit reason: None 619s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v2 619s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-nrenh16w" follows: 619s =========> 619s [2026-01-30T05:41:36+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:36+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v1 619s [2026-01-30T05:41:36+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v1 619s [2026-01-30T05:41:36+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:36+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:36+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v2 with ID kind-_testDockerLogsFn/instance-nrenh16w to 1 619s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 619s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:41:37: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-nrenh16w. 619s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v3 619s Exit reason: None 619s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v5 619s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-nrenh16w" follows: 619s =========> 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4 619s [2026-01-30T05:41:37+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:37+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:37+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v5 with ID kind-_testDockerLogsFn/instance-nrenh16w to 0 619s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v6 is completely failed 619s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:41:38: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 619s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 619s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v6 619s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 619s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 619s INFO  toil.lib.history:history.py:530 Workflow 7a5e7e64-2116-4e65-b211-ad046a85c63d stopped. Success: False 619s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux_Stream0/jobstore) 619s __ TestSingleMachinePromisedRequirements.testPromisesWithJobStoreFileObjects ___ 619s [gw0] linux -- Python 3.14.2 /usr/bin/python3.14 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 619s result: TResult | None = func() 619s ~~~~^^ 619s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 619s lambda: runtest_hook(item=item, **kwds), 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 619s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 619s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 619s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 619s raise exception 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 619s yield 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 619s return (yield) 619s ^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 619s return result.get_result() 619s ~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 619s raise exc.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 619s res = yield 619s ^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 619s return (yield) 619s ^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 619s res = hook_impl.function(*args) 619s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 619s item.runtest() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 619s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 619s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 619s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 619s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 619s raise exception 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 619s res = hook_impl.function(*args) 619s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 619s result = testfunction(**testargs) 619s File "/usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py", line 145, in testPromisesWithJobStoreFileObjects 619s Job.Runner.startToil(F1, self.getOptions(tmp_path, caching=caching)) 619s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 619s return toil.start(job) 619s ~~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 619s return self._runMainLoop(rootJobDescription) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 619s ).run() 619s ~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 619s raise FailedJobsException( 619s ...<3 lines>... 619s ) 619s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore' contains 2 failed jobs: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8, '_writer' kind-_writer/instance-yk1rpfbw v4 619s Log from job "'_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8" follows: 619s =========> 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'c8b78540-44ef-4d4f-b67e-7bdbf1a1adac', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': True, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmplo15ag5f', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/deferred/func3ipu26c2 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.worker] Parsed job description 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore'. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6) from description '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6) with ID (kind-EncapsulatedJob/instance-8yqn9nyw). 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6) with ID (kind-EncapsulatedJob/instance-8yqn9nyw) which wants 2147483648 of our 98062798848 bytes. 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98062798848 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98062798848 bytes 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:21+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 used 10.15x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:21+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 619s self.evaluatePromisedRequirements() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 619s ].getValue() 619s ~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 619s return func(*self._args) 619s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 619s 619s [2026-01-30T05:43:21+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [pydot] pydot initializing 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [pydot] pydot 4.0.1 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [pydot.core] pydot core module initializing 619s <========= 619s ----------------------------- Captured stderr call ----------------------------- 619s [2026-01-30T05:43:18+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:18+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:18+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:18+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:18+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:18+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:18+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:18+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.common] Initialized default configuration: {"config_version": 1.0} 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.batchSystems.options] Add options for aws_batch batch system 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.batchSystems.options] Add options for single_machine batch system 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.batchSystems.options] Add options for grid_engine batch system 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.batchSystems.options] Add options for lsf batch system 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.batchSystems.options] Add options for slurm batch system 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.batchSystems.options] Add options for torque batch system 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'asyncio', 'cachecontrol', 'concurrent', 'boto', 'humanfriendly', 'test', 'rdflib', 'salad', 'requests', 'werkzeug', 'debugWorkflow', 'botocore', 'urllib3', 'boto3', 'cwltest', 'docker', 'dill', 'bcdocs'} 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.statsAndLogging] Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'asyncio', 'cachecontrol', 'concurrent', 'boto', 'humanfriendly', 'test', 'rdflib', 'salad', 'requests', 'werkzeug', 'debugWorkflow', 'botocore', 'urllib3', 'boto3', 'cwltest', 'docker', 'dill', 'bcdocs'} 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.statsAndLogging] Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.common] Initialized default configuration: {"config_version": 1.0} 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.batchSystems.options] Add options for aws_batch batch system 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.batchSystems.options] Add options for single_machine batch system 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.batchSystems.options] Add options for grid_engine batch system 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.batchSystems.options] Add options for lsf batch system 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.batchSystems.options] Add options for slurm batch system 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.batchSystems.options] Add options for torque batch system 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.common] Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': None, 'logRotating': False, 'colored_logs': True, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'onSuccess', 'cleanWorkDir': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'coalesceStatusCalls': True, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'memory_is_product': False, 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'symlinkImports': True, 'moveOutputs': False, 'caching': True, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'maxNodes': [10], 'minNodes': [0], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'metrics': False, 'assume_zero_overhead': False, 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': False, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, 'publish_workflow_metrics': None, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'linkImports': None, 'moveExports': None, 'enableCaching': None, 'not_strict': False, 'enable_dev': False, 'enable_ext': False, 'quiet': False, 'basedir': None, 'outdir': None, 'log_dir': '', 'user_space_docker_cmd': None, 'singularity': False, 'podman': False, 'no_container': False, 'rm_container': True, 'custom_net': None, 'record_container_id': False, 'cidfile_dir': None, 'cidfile_prefix': None, 'no_prepull': False, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'beta_dependency_resolvers_configuration': None, 'beta_dependencies_directory': None, 'beta_use_biocontainers': None, 'beta_conda_dependencies': None, 'tmpdir_prefix': None, 'tmp_outdir_prefix': None, 'force_docker_pull': False, 'no_match_user': False, 'no_read_only': False, 'strict_memory_limit': False, 'strict_cpu_limit': False, 'relax_path_checks': False, 'default_container': None, 'do_validate': True, 'fast_parser': False, 'compute_checksum': True, 'eval_timeout': 20, 'overrides': None, 'mpi_config_file': None, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'cwl_default_ram': True, 'cwl_min_ram': None, 'destBucket': None, 'cachedir': None, 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto', 'all_call_outputs': None, 'strict': False, 'quant_check': True, 'run_imports_on_workers': False, 'import_workers_batchsize': 1073741824, 'import_workers_disk': 1048576} 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore'. 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.jobStores.abstractJobStore] The workflow ID is: 'c8b78540-44ef-4d4f-b67e-7bdbf1a1adac' 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of c8b78540-44ef-4d4f-b67e-7bdbf1a1adac in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.lib.history] Workflow c8b78540-44ef-4d4f-b67e-7bdbf1a1adac is a run of 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.common] Using the single machine batch system 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.common] Created the workflow directory for this machine at /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b 619s [2026-01-30T05:43:19+0000] [Thread-95 (daddy)] [D] [toil.batchSystems.singleMachine] Started daddy thread for batch system 247544560384032. 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Started batch system 247544560384032 in normal mode. 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.common] User script ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.common] No user script to auto-deploy. 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.common] Written the environment for the jobs to the environment file 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.common] Caching all jobs in job store 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.common] 0 jobs downloaded. 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-f4c2ed41e0c3468b8d865a6f5b6e16c3/stream for result of '_writer' TemporaryID(3930fbd3-906c-4ae2-92dc-b98e496fc614) v0 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Saving graph of 5 jobs, 5 non-service, 5 new 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Processing job 'Job' kind-Job/instance-k81ojz2c v0 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Processing job '_follower' kind-_follower/instance-zu1yjb6s v0 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-f5eacbf71a834ab79bfdd2efd57d525f/stream for result of '_writer' kind-_writer/instance-yk1rpfbw v0 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-c9d288718d5a428d912dfc4744d9cf31/stream for result of '_writer' kind-_writer/instance-5x0kw7o2 v0 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v0 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-5x0kw7o2 v0 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-yk1rpfbw v0 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] New job version: 'Job' kind-Job/instance-k81ojz2c v1 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-_follower/instance-zu1yjb6s v1 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-5x0kw7o2 v1 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-yk1rpfbw v1 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'c8b78540-44ef-4d4f-b67e-7bdbf1a1adac', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': True, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmplo15ag5f', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.bus] Listening for message topic: toil.bus.JobUpdatedMessage 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.toilState] Found job to run: kind-_writer/instance-yk1rpfbw, with body: True, with checkpoint: False, with services: False, with no next successors: False 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-yk1rpfbw', result_status=0) 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.leader] Found 1 jobs to start and 0 jobs with successors to run 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.leader] Checked batch system has no running jobs and no updated jobs 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.serviceManager] Initializing service manager 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-yk1rpfbw v1 with result status: 0 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore kind-_writer/instance-yk1rpfbw with disk: 2.0 Gi, memory: 2.0 Gi, cores: 2.0, accelerators: [], preemptible: False 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.leader] Issued job '_writer' kind-_writer/instance-yk1rpfbw v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 2, accelerators: [], preemptible: False 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_writer', job_id='kind-_writer/instance-yk1rpfbw', toil_batch_id=1) 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 619s [2026-01-30T05:43:19+0000] [Thread-95 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore kind-_writer/instance-yk1rpfbw 619s [2026-01-30T05:43:19+0000] [Thread-95 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 1 as child 10328 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'concurrent', 'boto', 'docker', 'boto3', 'botocore', 'dill', 'urllib3', 'requests', 'asyncio'} 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.worker] Worker started for job _writer... 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.common] Obtained node ID d997a28e7a334b4298ab4a55574a1a13 from file /var/lib/dbus/machine-id 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/6a5d/worker_log.txt 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/deferred/funcs9_c2iqt 619s [2026-01-30T05:43:20+0000] [Thread-95 (daddy)] [D] [toil.batchSystems.singleMachine] Child 10328 for job 1 succeeded 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 1 with exit value: 0 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.leader] Job ended: '_writer' kind-_writer/instance-yk1rpfbw v1 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_writer', job_id='kind-_writer/instance-yk1rpfbw', exit_code=0) 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=1, external_batch_id='10328', batch_system='SingleMachineBatchSystem') 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.leader] Job '_writer' kind-_writer/instance-yk1rpfbw v1 continues to exist (i.e. has more to do) 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-yk1rpfbw', result_status=0) 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.leader] Added job: '_writer' kind-_writer/instance-yk1rpfbw v4 to updated jobs 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-yk1rpfbw v4 with result status: 0 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.leader] Job: kind-_writer/instance-yk1rpfbw has 1 successors to schedule 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.toilState] Successors: 1 more for kind-_writer/instance-yk1rpfbw, now have 1 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.leader] Added job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 as coming after job '_writer' kind-_writer/instance-yk1rpfbw v4 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-8yqn9nyw with disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil.leader] Issued job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 with job batch system ID: 2 and disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-8yqn9nyw', toil_batch_id=2) 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 619s [2026-01-30T05:43:20+0000] [Thread-95 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-8yqn9nyw 619s [2026-01-30T05:43:20+0000] [Thread-95 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 2 as child 10388 619s [2026-01-30T05:43:20+0000] [Thread-98 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:43:20: Job '_writer' kind-_writer/instance-yk1rpfbw v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:20+0000] [Thread-98 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:43:20: Job '_writer' kind-_writer/instance-yk1rpfbw v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:20+0000] [Thread-98 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Received Toil worker log. Disable debug level logging to hide this output 619s [2026-01-30T05:43:20+0000] [Thread-98 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Log from job "JobFunctionWrappingJob" follows: 619s =========> 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'c8b78540-44ef-4d4f-b67e-7bdbf1a1adac', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': True, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmplo15ag5f', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/deferred/funcs9_c2iqt 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.worker] Parsed job description 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-yk1rpfbw v1 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-yk1rpfbw v1) from description '_writer' kind-_writer/instance-yk1rpfbw v1 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-yk1rpfbw v1) with ID (kind-_writer/instance-yk1rpfbw). 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_writer' kind-_writer/instance-yk1rpfbw v1) with ID (kind-_writer/instance-yk1rpfbw) which wants 2147483648 of our 98062798848 bytes. 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98062798848 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 0 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98062798848 bytes 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Loading user function _writer from module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Hardlinked file /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/6a5d/job/tmpjoy4vlbe.tmp into cache at /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/cache-c8b78540-44ef-4d4f-b67e-7bdbf1a1adac/tmpmwxgd5nm0183354c05a4307208b8dcf4b03c2577322be6eb; deferring write to job store 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-f4c2ed41e0c3468b8d865a6f5b6e16c3/stream from Job('_writer' kind-_writer/instance-yk1rpfbw v1) with a 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-f5eacbf71a834ab79bfdd2efd57d525f/stream from Job('_writer' kind-_writer/instance-yk1rpfbw v1) with a 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-yk1rpfbw v1 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-yk1rpfbw v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-yk1rpfbw v1 forked from '_writer' kind-_writer/instance-yk1rpfbw v1 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-yk1rpfbw v2 619s [2026-01-30T05:43:19+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-yk1rpfbw v2 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-yk1rpfbw v2 would chain to ID kind-_writer/instance-5x0kw7o2 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Chaining from '_writer' kind-_writer/instance-yk1rpfbw v2 to '_writer' kind-_writer/instance-5x0kw7o2 v1 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] '_writer' kind-_writer/instance-5x0kw7o2 v1 is adopting successor phases from '_writer' kind-_writer/instance-yk1rpfbw v2 of: [] 619s [2026-01-30T05:43:19+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Actually executing upload for file files/for-job/kind-_writer/instance-yk1rpfbw/file-4ceb65b528a44fc18931b05e6ed98ea8/tmpjoy4vlbe.tmp 619s [2026-01-30T05:43:19+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-yk1rpfbw v1 619s [2026-01-30T05:43:19+0000] [Thread-2 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-yk1rpfbw v2 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-yk1rpfbw v2) with ID (kind-_writer/instance-yk1rpfbw). 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-yk1rpfbw v2 forked from '_writer' kind-_writer/instance-yk1rpfbw v2 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-yk1rpfbw v3 619s [2026-01-30T05:43:19+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.worker] Starting the next job 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-yk1rpfbw v3 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-yk1rpfbw v3) from description '_writer' kind-_writer/instance-yk1rpfbw v3 619s [2026-01-30T05:43:19+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-yk1rpfbw v2 619s [2026-01-30T05:43:19+0000] [Thread-3 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-yk1rpfbw v3 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-yk1rpfbw v3) with ID (kind-_writer/instance-yk1rpfbw). 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_writer' kind-_writer/instance-yk1rpfbw v3) with ID (kind-_writer/instance-yk1rpfbw) which wants 2147483648 of our 98062798848 bytes. 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98062798848 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1024 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98062798848 bytes 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Loading user function _writer from module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Hardlinked file /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/6a5d/job/tmpx54n622a.tmp into cache at /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/cache-c8b78540-44ef-4d4f-b67e-7bdbf1a1adac/tmpg3j3dz259599e6272c0bbd004147735af6e161533f750082; deferring write to job store 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-c9d288718d5a428d912dfc4744d9cf31/stream from Job('_writer' kind-_writer/instance-yk1rpfbw v3) with a 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-yk1rpfbw v3 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-yk1rpfbw v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-yk1rpfbw v3 forked from '_writer' kind-_writer/instance-yk1rpfbw v3 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-yk1rpfbw v4 619s [2026-01-30T05:43:19+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-yk1rpfbw v4 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-yk1rpfbw v4 would chain to ID kind-EncapsulatedJob/instance-8yqn9nyw 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.worker] Preemptibility is different for the next job, returning to the leader 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Not chaining from job '_writer' kind-_writer/instance-yk1rpfbw v4 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/6a5d. Set --cleanWorkDir to retain this log 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 0.335292 seconds 619s [2026-01-30T05:43:19+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Actually executing upload for file files/for-job/kind-_writer/instance-yk1rpfbw/file-a82fe4b4cb0a41dba68c118bb0194965/tmpx54n622a.tmp 619s [2026-01-30T05:43:19+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-yk1rpfbw v3 619s [2026-01-30T05:43:19+0000] [Thread-4 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-yk1rpfbw v4 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [pydot] pydot initializing 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [pydot] pydot 4.0.1 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [pydot.core] pydot core module initializing 619s <========= 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'urllib3', 'boto', 'requests', 'concurrent', 'docker', 'asyncio', 'botocore', 'dill', 'boto3'} 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.worker] Worker started for job EncapsulatedJob... 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.common] Obtained node ID d997a28e7a334b4298ab4a55574a1a13 from file /var/lib/dbus/machine-id 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/39dc/worker_log.txt 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v4 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/deferred/funcuod52jvd 619s [2026-01-30T05:43:21+0000] [Thread-95 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-8yqn9nyw. 619s [2026-01-30T05:43:21+0000] [Thread-95 (daddy)] [D] [toil.batchSystems.singleMachine] Child 10388 for job 2 succeeded 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 2 with exit value: 1 619s [2026-01-30T05:43:21+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 619s Exit reason: None 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-8yqn9nyw', exit_code=1) 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=2, external_batch_id='10388', batch_system='SingleMachineBatchSystem') 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.leader] Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 continues to exist (i.e. has more to do) 619s [2026-01-30T05:43:21+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v4 619s [2026-01-30T05:43:21+0000] [MainThread] [W] [toil.leader] Log from job "kind-EncapsulatedJob/instance-8yqn9nyw" follows: 619s =========> 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'c8b78540-44ef-4d4f-b67e-7bdbf1a1adac', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': True, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmplo15ag5f', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/deferred/funcuod52jvd 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.worker] Parsed job description 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil.worker] Working on job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1) from description 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1) with ID (kind-EncapsulatedJob/instance-8yqn9nyw). 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1) with ID (kind-EncapsulatedJob/instance-8yqn9nyw) which wants 1000000 of our 98062798848 bytes. 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98062798848 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 1000000 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98062798848 bytes 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 forked from 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.job] Skip ahead to job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v2 619s [2026-01-30T05:43:20+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 619s [2026-01-30T05:43:20+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v2 used 9.94x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil.worker] Completed body for 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v2 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.worker] 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v2 would chain to ID kind-_follower/instance-zu1yjb6s 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil.worker] Chaining from 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v2 to '_follower' kind-_follower/instance-zu1yjb6s v1 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.job] '_follower' kind-_follower/instance-zu1yjb6s v1 is adopting successor phases from 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v2 of: [{'kind-Job/instance-k81ojz2c'}] 619s [2026-01-30T05:43:20+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 619s [2026-01-30T05:43:20+0000] [Thread-2 (startCommitThread)] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v2 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v2) with ID (kind-EncapsulatedJob/instance-8yqn9nyw). 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v2 forked from '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v2 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3 619s [2026-01-30T05:43:20+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.worker] Starting the next job 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore'. 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3) from description '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3 619s [2026-01-30T05:43:20+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v2 619s [2026-01-30T05:43:20+0000] [Thread-3 (startCommitThread)] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3) with ID (kind-EncapsulatedJob/instance-8yqn9nyw). 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3) with ID (kind-EncapsulatedJob/instance-8yqn9nyw) which wants 1000000 of our 98062798848 bytes. 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98062798848 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 1000000 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98062798848 bytes 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:20+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3 used 10.28x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:20+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 619s self.evaluatePromisedRequirements() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 619s ].getValue() 619s ~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 619s return func(*self._args) 619s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 619s 619s [2026-01-30T05:43:20+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [pydot] pydot initializing 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [pydot] pydot 4.0.1 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [pydot.core] pydot core module initializing 619s <========= 619s [2026-01-30T05:43:21+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v4 with ID kind-EncapsulatedJob/instance-8yqn9nyw to 1 619s [2026-01-30T05:43:21+0000] [MainThread] [W] [toil.job] We have increased the default memory of the failed job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v4 to 2147483648 bytes 619s [2026-01-30T05:43:21+0000] [MainThread] [W] [toil.job] We have increased the disk of the failed job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v4 to the default of 2147483648 bytes 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v5 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-8yqn9nyw', result_status=1) 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.leader] Added job: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v5 to updated jobs 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.leader] Updating status of job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v5 with result status: 1 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-8yqn9nyw with disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil.leader] Issued job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v5 with job batch system ID: 3 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-8yqn9nyw', toil_batch_id=3) 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 619s [2026-01-30T05:43:21+0000] [Thread-95 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-8yqn9nyw 619s [2026-01-30T05:43:21+0000] [Thread-95 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 3 as child 10429 619s [2026-01-30T05:43:21+0000] [Thread-98 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:43:21: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 619s [2026-01-30T05:43:21+0000] [Thread-98 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:43:21: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v2 used 9.94x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:21+0000] [Thread-98 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:43:21: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 619s [2026-01-30T05:43:21+0000] [Thread-98 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:43:21: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3 used 10.28x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'boto3', 'concurrent', 'dill', 'urllib3', 'requests', 'docker', 'asyncio', 'boto', 'botocore'} 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.worker] Worker started for job _follower... 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.common] Obtained node ID d997a28e7a334b4298ab4a55574a1a13 from file /var/lib/dbus/machine-id 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/65e6/worker_log.txt 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v7 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/deferred/func3ipu26c2 619s [2026-01-30T05:43:22+0000] [Thread-95 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-8yqn9nyw. 619s [2026-01-30T05:43:22+0000] [Thread-95 (daddy)] [D] [toil.batchSystems.singleMachine] Child 10429 for job 3 succeeded 619s [2026-01-30T05:43:22+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 3 with exit value: 1 619s [2026-01-30T05:43:22+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v5 619s Exit reason: None 619s [2026-01-30T05:43:22+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-8yqn9nyw', exit_code=1) 619s [2026-01-30T05:43:22+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=3, external_batch_id='10429', batch_system='SingleMachineBatchSystem') 619s [2026-01-30T05:43:22+0000] [MainThread] [D] [toil.leader] Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v5 continues to exist (i.e. has more to do) 619s [2026-01-30T05:43:22+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v7 619s [2026-01-30T05:43:22+0000] [MainThread] [W] [toil.leader] Log from job "kind-EncapsulatedJob/instance-8yqn9nyw" follows: 619s =========> 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'c8b78540-44ef-4d4f-b67e-7bdbf1a1adac', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': True, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmplo15ag5f', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/deferred/func3ipu26c2 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.worker] Parsed job description 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore'. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6) from description '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6) with ID (kind-EncapsulatedJob/instance-8yqn9nyw). 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6) with ID (kind-EncapsulatedJob/instance-8yqn9nyw) which wants 2147483648 of our 98062798848 bytes. 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98062798848 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98062798848 bytes 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:21+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 used 10.15x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:21+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 619s self.evaluatePromisedRequirements() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 619s ].getValue() 619s ~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 619s return func(*self._args) 619s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 619s 619s [2026-01-30T05:43:21+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [pydot] pydot initializing 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [pydot] pydot 4.0.1 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [pydot.core] pydot core module initializing 619s <========= 619s [2026-01-30T05:43:22+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v7 with ID kind-EncapsulatedJob/instance-8yqn9nyw to 0 619s [2026-01-30T05:43:22+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8 619s [2026-01-30T05:43:22+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-8yqn9nyw', result_status=1) 619s [2026-01-30T05:43:22+0000] [MainThread] [D] [toil.leader] Added job: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8 to updated jobs 619s [2026-01-30T05:43:22+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s [2026-01-30T05:43:22+0000] [MainThread] [D] [toil.leader] Updating status of job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8 with result status: 1 619s [2026-01-30T05:43:22+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-8yqn9nyw') 619s [2026-01-30T05:43:22+0000] [MainThread] [D] [toil.leader] Found new failed successors: kind-Job/instance-k81ojz2c of job: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8 619s [2026-01-30T05:43:22+0000] [MainThread] [D] [toil.leader] Totally failed job: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8 is marking direct predecessor: '_writer' kind-_writer/instance-yk1rpfbw v4 as having failed jobs 619s [2026-01-30T05:43:22+0000] [MainThread] [D] [toil.leader] Cleaning the predecessors of kind-EncapsulatedJob/instance-8yqn9nyw 619s [2026-01-30T05:43:22+0000] [MainThread] [D] [toil.toilState] Successors: one fewer for kind-_writer/instance-yk1rpfbw, now have 0 619s [2026-01-30T05:43:22+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-yk1rpfbw', result_status=0) 619s [2026-01-30T05:43:22+0000] [MainThread] [W] [toil.leader] Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8 is completely failed 619s [2026-01-30T05:43:22+0000] [Thread-98 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:43:22: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:22+0000] [Thread-98 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:43:22: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 used 10.15x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:24+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s [2026-01-30T05:43:24+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-yk1rpfbw v4 with result status: 0 619s [2026-01-30T05:43:24+0000] [MainThread] [D] [toil.leader] Job kind-_writer/instance-yk1rpfbw is being processed as completely failed 619s [2026-01-30T05:43:24+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_writer', job_id='kind-_writer/instance-yk1rpfbw') 619s [2026-01-30T05:43:24+0000] [MainThread] [D] [toil.leader] Found new failed successors: of job: '_writer' kind-_writer/instance-yk1rpfbw v4 619s [2026-01-30T05:43:26+0000] [MainThread] [D] [toil.leader] Finished the main loop: no jobs left to run. 619s [2026-01-30T05:43:26+0000] [MainThread] [D] [toil.serviceManager] Waiting for service manager thread to finish ... 619s [2026-01-30T05:43:26+0000] [Thread-97 (__start_services)] [D] [toil.serviceManager] Received signal to quit starting services. 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.serviceManager] ... finished shutting down the service manager. Took 1.1180410385131836 seconds 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.statsAndLogging] Waiting for stats and logging collator thread to finish ... 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.statsAndLogging] ... finished collating stats and logs. Took 0.006304025650024414 seconds 619s [2026-01-30T05:43:27+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 619s [2026-01-30T05:43:27+0000] [MainThread] [I] [toil.leader] Finished toil run with 2 failed jobs. 619s [2026-01-30T05:43:27+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8 '_writer' kind-_writer/instance-yk1rpfbw v4 619s [2026-01-30T05:43:27+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 619s [2026-01-30T05:43:27+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.common] Shutting down batch system ... 619s [2026-01-30T05:43:27+0000] [Thread-95 (daddy)] [D] [toil.batchSystems.singleMachine] Daddy thread cleaning up 0 remaining children for batch system 247544560384032... 619s [2026-01-30T05:43:27+0000] [Thread-95 (daddy)] [D] [toil.batchSystems.singleMachine] Daddy thread for batch system 247544560384032 finishing because no children should now exist 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Attempting worker cleanup 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.deferred] Cleaning up deferred functions system 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/deferred/funcbbx1ay_k 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/deferred/funcbbx1ay_k 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Connecting to latest caching database cache-0.db for cleanup 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Deleting workflow directory /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Deleting coordination directory /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.common] ... finished shutting down the batch system in 0.014912128448486328 seconds. 619s [2026-01-30T05:43:27+0000] [MainThread] [I] [toil.lib.history] Workflow c8b78540-44ef-4d4f-b67e-7bdbf1a1adac stopped. Success: False 619s ------------------------------ Captured log call ------------------------------- 619s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s DEBUG  toil.common:common.py:796 Initialized default configuration: {"config_version": 1.0} 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for aws_batch batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for single_machine batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for grid_engine batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for lsf batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for slurm batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for torque batch system 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:488 Suppressing the following loggers: {'asyncio', 'cachecontrol', 'concurrent', 'boto', 'humanfriendly', 'test', 'rdflib', 'salad', 'requests', 'werkzeug', 'debugWorkflow', 'botocore', 'urllib3', 'boto3', 'cwltest', 'docker', 'dill', 'bcdocs'} 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:447 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:488 Suppressing the following loggers: {'asyncio', 'cachecontrol', 'concurrent', 'boto', 'humanfriendly', 'test', 'rdflib', 'salad', 'requests', 'werkzeug', 'debugWorkflow', 'botocore', 'urllib3', 'boto3', 'cwltest', 'docker', 'dill', 'bcdocs'} 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:447 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 619s DEBUG  toil.common:common.py:796 Initialized default configuration: {"config_version": 1.0} 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for aws_batch batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for single_machine batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for grid_engine batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for lsf batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for slurm batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for torque batch system 619s DEBUG  toil.common:common.py:1006 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': None, 'logRotating': False, 'colored_logs': True, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'onSuccess', 'cleanWorkDir': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'coalesceStatusCalls': True, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'memory_is_product': False, 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'symlinkImports': True, 'moveOutputs': False, 'caching': True, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'maxNodes': [10], 'minNodes': [0], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'metrics': False, 'assume_zero_overhead': False, 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': False, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, 'publish_workflow_metrics': None, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'linkImports': None, 'moveExports': None, 'enableCaching': None, 'not_strict': False, 'enable_dev': False, 'enable_ext': False, 'quiet': False, 'basedir': None, 'outdir': None, 'log_dir': '', 'user_space_docker_cmd': None, 'singularity': False, 'podman': False, 'no_container': False, 'rm_container': True, 'custom_net': None, 'record_container_id': False, 'cidfile_dir': None, 'cidfile_prefix': None, 'no_prepull': False, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'beta_dependency_resolvers_configuration': None, 'beta_dependencies_directory': None, 'beta_use_biocontainers': None, 'beta_conda_dependencies': None, 'tmpdir_prefix': None, 'tmp_outdir_prefix': None, 'force_docker_pull': False, 'no_match_user': False, 'no_read_only': False, 'strict_memory_limit': False, 'strict_cpu_limit': False, 'relax_path_checks': False, 'default_container': None, 'do_validate': True, 'fast_parser': False, 'compute_checksum': True, 'eval_timeout': 20, 'overrides': None, 'mpi_config_file': None, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'cwl_default_ram': True, 'cwl_min_ram': None, 'destBucket': None, 'cachedir': None, 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto', 'all_call_outputs': None, 'strict': False, 'quant_check': True, 'run_imports_on_workers': False, 'import_workers_batchsize': 1073741824, 'import_workers_disk': 1048576} 619s DEBUG  toil.jobStores.fileJobStore:fileJobStore.py:93 Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore'. 619s DEBUG  toil.jobStores.abstractJobStore:abstractJobStore.py:212 The workflow ID is: 'c8b78540-44ef-4d4f-b67e-7bdbf1a1adac' 619s INFO  toil.lib.history:history.py:369 Recording workflow creation of c8b78540-44ef-4d4f-b67e-7bdbf1a1adac in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore 619s INFO  toil.lib.history:history.py:399 Workflow c8b78540-44ef-4d4f-b67e-7bdbf1a1adac is a run of 619s DEBUG  toil.common:common.py:1346 Using the single machine batch system 619s DEBUG  toil.common:common.py:1723 Created the workflow directory for this machine at /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:247 Started daddy thread for batch system 247544560384032. 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:229 Started batch system 247544560384032 in normal mode. 619s DEBUG  toil.common:common.py:1367 User script ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. 619s DEBUG  toil.common:common.py:1409 No user script to auto-deploy. 619s DEBUG  toil.common:common.py:1576 Written the environment for the jobs to the environment file 619s DEBUG  toil.common:common.py:1580 Caching all jobs in job store 619s DEBUG  toil.common:common.py:1584 0 jobs downloaded. 619s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-f4c2ed41e0c3468b8d865a6f5b6e16c3/stream for result of '_writer' TemporaryID(3930fbd3-906c-4ae2-92dc-b98e496fc614) v0 619s DEBUG  toil.job:job.py:3000 Saving graph of 5 jobs, 5 non-service, 5 new 619s DEBUG  toil.job:job.py:3023 Processing job 'Job' kind-Job/instance-k81ojz2c v0 619s DEBUG  toil.job:job.py:3023 Processing job '_follower' kind-_follower/instance-zu1yjb6s v0 619s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-f5eacbf71a834ab79bfdd2efd57d525f/stream for result of '_writer' kind-_writer/instance-yk1rpfbw v0 619s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-c9d288718d5a428d912dfc4744d9cf31/stream for result of '_writer' kind-_writer/instance-5x0kw7o2 v0 619s DEBUG  toil.job:job.py:3023 Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v0 619s DEBUG  toil.job:job.py:3023 Processing job '_writer' kind-_writer/instance-5x0kw7o2 v0 619s DEBUG  toil.job:job.py:3023 Processing job '_writer' kind-_writer/instance-yk1rpfbw v0 619s DEBUG  toil.job:job.py:1507 New job version: 'Job' kind-Job/instance-k81ojz2c v1 619s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-_follower/instance-zu1yjb6s v1 619s DEBUG  toil.job:job.py:1507 New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 619s DEBUG  toil.job:job.py:1507 New job version: '_writer' kind-_writer/instance-5x0kw7o2 v1 619s DEBUG  toil.job:job.py:1507 New job version: '_writer' kind-_writer/instance-yk1rpfbw v1 619s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s DEBUG  toil:__init__.py:481 Configuration: {'cwl': False, 'workflowID': 'c8b78540-44ef-4d4f-b67e-7bdbf1a1adac', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': True, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmplo15ag5f', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 619s DEBUG  toil.bus:bus.py:403 Listening for message topic: toil.bus.JobUpdatedMessage 619s DEBUG  toil.toilState:toilState.py:322 Found job to run: kind-_writer/instance-yk1rpfbw, with body: True, with checkpoint: False, with services: False, with no next successors: False 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-yk1rpfbw', result_status=0) 619s DEBUG  toil.leader:leader.py:145 Found 1 jobs to start and 0 jobs with successors to run 619s DEBUG  toil.leader:leader.py:157 Checked batch system has no running jobs and no updated jobs 619s DEBUG  toil.serviceManager:serviceManager.py:35 Initializing service manager 619s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-yk1rpfbw v1 with result status: 0 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore kind-_writer/instance-yk1rpfbw with disk: 2.0 Gi, memory: 2.0 Gi, cores: 2.0, accelerators: [], preemptible: False 619s INFO  toil.leader:leader.py:1132 Issued job '_writer' kind-_writer/instance-yk1rpfbw v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 2, accelerators: [], preemptible: False 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_writer', job_id='kind-_writer/instance-yk1rpfbw', toil_batch_id=1) 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore kind-_writer/instance-yk1rpfbw 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 1 as child 10328 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 10328 for job 1 succeeded 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 1 with exit value: 0 619s DEBUG  toil.leader:leader.py:846 Job ended: '_writer' kind-_writer/instance-yk1rpfbw v1 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_writer', job_id='kind-_writer/instance-yk1rpfbw', exit_code=0) 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=1, external_batch_id='10328', batch_system='SingleMachineBatchSystem') 619s DEBUG  toil.leader:leader.py:1455 Job '_writer' kind-_writer/instance-yk1rpfbw v1 continues to exist (i.e. has more to do) 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-yk1rpfbw', result_status=0) 619s DEBUG  toil.leader:leader.py:1620 Added job: '_writer' kind-_writer/instance-yk1rpfbw v4 to updated jobs 619s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 619s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-yk1rpfbw v4 with result status: 0 619s DEBUG  toil.leader:leader.py:506 Job: kind-_writer/instance-yk1rpfbw has 1 successors to schedule 619s DEBUG  toil.toilState:toilState.py:264 Successors: 1 more for kind-_writer/instance-yk1rpfbw, now have 1 619s DEBUG  toil.leader:leader.py:476 Added job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 as coming after job '_writer' kind-_writer/instance-yk1rpfbw v4 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-8yqn9nyw with disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 619s INFO  toil.leader:leader.py:1132 Issued job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 with job batch system ID: 2 and disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-8yqn9nyw', toil_batch_id=2) 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-8yqn9nyw 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 2 as child 10388 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:43:20: Job '_writer' kind-_writer/instance-yk1rpfbw v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:43:20: Job '_writer' kind-_writer/instance-yk1rpfbw v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:98 Received Toil worker log. Disable debug level logging to hide this output 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:101 Log from job "JobFunctionWrappingJob" follows: 619s =========> 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'c8b78540-44ef-4d4f-b67e-7bdbf1a1adac', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': True, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmplo15ag5f', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/deferred/funcs9_c2iqt 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.worker] Parsed job description 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-yk1rpfbw v1 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-yk1rpfbw v1) from description '_writer' kind-_writer/instance-yk1rpfbw v1 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-yk1rpfbw v1) with ID (kind-_writer/instance-yk1rpfbw). 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_writer' kind-_writer/instance-yk1rpfbw v1) with ID (kind-_writer/instance-yk1rpfbw) which wants 2147483648 of our 98062798848 bytes. 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98062798848 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 0 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98062798848 bytes 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Loading user function _writer from module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Hardlinked file /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/6a5d/job/tmpjoy4vlbe.tmp into cache at /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/cache-c8b78540-44ef-4d4f-b67e-7bdbf1a1adac/tmpmwxgd5nm0183354c05a4307208b8dcf4b03c2577322be6eb; deferring write to job store 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-f4c2ed41e0c3468b8d865a6f5b6e16c3/stream from Job('_writer' kind-_writer/instance-yk1rpfbw v1) with a 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-f5eacbf71a834ab79bfdd2efd57d525f/stream from Job('_writer' kind-_writer/instance-yk1rpfbw v1) with a 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-yk1rpfbw v1 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-yk1rpfbw v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-yk1rpfbw v1 forked from '_writer' kind-_writer/instance-yk1rpfbw v1 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-yk1rpfbw v2 619s [2026-01-30T05:43:19+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-yk1rpfbw v2 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-yk1rpfbw v2 would chain to ID kind-_writer/instance-5x0kw7o2 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Chaining from '_writer' kind-_writer/instance-yk1rpfbw v2 to '_writer' kind-_writer/instance-5x0kw7o2 v1 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] '_writer' kind-_writer/instance-5x0kw7o2 v1 is adopting successor phases from '_writer' kind-_writer/instance-yk1rpfbw v2 of: [] 619s [2026-01-30T05:43:19+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Actually executing upload for file files/for-job/kind-_writer/instance-yk1rpfbw/file-4ceb65b528a44fc18931b05e6ed98ea8/tmpjoy4vlbe.tmp 619s [2026-01-30T05:43:19+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-yk1rpfbw v1 619s [2026-01-30T05:43:19+0000] [Thread-2 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-yk1rpfbw v2 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-yk1rpfbw v2) with ID (kind-_writer/instance-yk1rpfbw). 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-yk1rpfbw v2 forked from '_writer' kind-_writer/instance-yk1rpfbw v2 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-yk1rpfbw v3 619s [2026-01-30T05:43:19+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.worker] Starting the next job 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-yk1rpfbw v3 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-yk1rpfbw v3) from description '_writer' kind-_writer/instance-yk1rpfbw v3 619s [2026-01-30T05:43:19+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-yk1rpfbw v2 619s [2026-01-30T05:43:19+0000] [Thread-3 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-yk1rpfbw v3 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-yk1rpfbw v3) with ID (kind-_writer/instance-yk1rpfbw). 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_writer' kind-_writer/instance-yk1rpfbw v3) with ID (kind-_writer/instance-yk1rpfbw) which wants 2147483648 of our 98062798848 bytes. 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98062798848 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1024 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98062798848 bytes 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Loading user function _writer from module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Hardlinked file /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/6a5d/job/tmpx54n622a.tmp into cache at /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/cache-c8b78540-44ef-4d4f-b67e-7bdbf1a1adac/tmpg3j3dz259599e6272c0bbd004147735af6e161533f750082; deferring write to job store 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-c9d288718d5a428d912dfc4744d9cf31/stream from Job('_writer' kind-_writer/instance-yk1rpfbw v3) with a 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-yk1rpfbw v3 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-yk1rpfbw v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-yk1rpfbw v3 forked from '_writer' kind-_writer/instance-yk1rpfbw v3 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-yk1rpfbw v4 619s [2026-01-30T05:43:19+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-yk1rpfbw v4 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-yk1rpfbw v4 would chain to ID kind-EncapsulatedJob/instance-8yqn9nyw 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [toil.worker] Preemptibility is different for the next job, returning to the leader 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Not chaining from job '_writer' kind-_writer/instance-yk1rpfbw v4 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/6a5d. Set --cleanWorkDir to retain this log 619s [2026-01-30T05:43:19+0000] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 0.335292 seconds 619s [2026-01-30T05:43:19+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Actually executing upload for file files/for-job/kind-_writer/instance-yk1rpfbw/file-a82fe4b4cb0a41dba68c118bb0194965/tmpx54n622a.tmp 619s [2026-01-30T05:43:19+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-yk1rpfbw v3 619s [2026-01-30T05:43:19+0000] [Thread-4 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-yk1rpfbw v4 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [pydot] pydot initializing 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [pydot] pydot 4.0.1 619s [2026-01-30T05:43:19+0000] [MainThread] [D] [pydot.core] pydot core module initializing 619s <========= 619s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-8yqn9nyw. 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 10388 for job 2 succeeded 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 2 with exit value: 1 619s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 619s Exit reason: None 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-8yqn9nyw', exit_code=1) 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=2, external_batch_id='10388', batch_system='SingleMachineBatchSystem') 619s DEBUG  toil.leader:leader.py:1455 Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 continues to exist (i.e. has more to do) 619s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v4 619s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-EncapsulatedJob/instance-8yqn9nyw" follows: 619s =========> 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'c8b78540-44ef-4d4f-b67e-7bdbf1a1adac', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': True, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmplo15ag5f', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/deferred/funcuod52jvd 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.worker] Parsed job description 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil.worker] Working on job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1) from description 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1) with ID (kind-EncapsulatedJob/instance-8yqn9nyw). 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1) with ID (kind-EncapsulatedJob/instance-8yqn9nyw) which wants 1000000 of our 98062798848 bytes. 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98062798848 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 1000000 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98062798848 bytes 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 forked from 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.job] Skip ahead to job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v2 619s [2026-01-30T05:43:20+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 619s [2026-01-30T05:43:20+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v2 used 9.94x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil.worker] Completed body for 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v2 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.worker] 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v2 would chain to ID kind-_follower/instance-zu1yjb6s 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil.worker] Chaining from 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v2 to '_follower' kind-_follower/instance-zu1yjb6s v1 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.job] '_follower' kind-_follower/instance-zu1yjb6s v1 is adopting successor phases from 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v2 of: [{'kind-Job/instance-k81ojz2c'}] 619s [2026-01-30T05:43:20+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 619s [2026-01-30T05:43:20+0000] [Thread-2 (startCommitThread)] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v2 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v2) with ID (kind-EncapsulatedJob/instance-8yqn9nyw). 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v2 forked from '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v2 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3 619s [2026-01-30T05:43:20+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.worker] Starting the next job 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore'. 619s [2026-01-30T05:43:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3) from description '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3 619s [2026-01-30T05:43:20+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v2 619s [2026-01-30T05:43:20+0000] [Thread-3 (startCommitThread)] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3) with ID (kind-EncapsulatedJob/instance-8yqn9nyw). 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3) with ID (kind-EncapsulatedJob/instance-8yqn9nyw) which wants 1000000 of our 98062798848 bytes. 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98062798848 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 1000000 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98062798848 bytes 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:20+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3 used 10.28x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:20+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 619s self.evaluatePromisedRequirements() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 619s ].getValue() 619s ~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 619s return func(*self._args) 619s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 619s 619s [2026-01-30T05:43:20+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [pydot] pydot initializing 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [pydot] pydot 4.0.1 619s [2026-01-30T05:43:20+0000] [MainThread] [D] [pydot.core] pydot core module initializing 619s <========= 619s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v4 with ID kind-EncapsulatedJob/instance-8yqn9nyw to 1 619s WARNING  toil.job:job.py:1413 We have increased the default memory of the failed job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v4 to 2147483648 bytes 619s WARNING  toil.job:job.py:1421 We have increased the disk of the failed job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v4 to the default of 2147483648 bytes 619s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v5 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-8yqn9nyw', result_status=1) 619s DEBUG  toil.leader:leader.py:1620 Added job: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v5 to updated jobs 619s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s DEBUG  toil.leader:leader.py:606 Updating status of job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v5 with result status: 1 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-8yqn9nyw with disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 619s INFO  toil.leader:leader.py:1132 Issued job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v5 with job batch system ID: 3 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-8yqn9nyw', toil_batch_id=3) 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-8yqn9nyw 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 3 as child 10429 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:43:21: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 619s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:43:21: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-8yqn9nyw v2 used 9.94x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:43:21: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 619s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:43:21: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v3 used 10.28x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-8yqn9nyw. 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 10429 for job 3 succeeded 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 3 with exit value: 1 619s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v5 619s Exit reason: None 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-8yqn9nyw', exit_code=1) 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=3, external_batch_id='10429', batch_system='SingleMachineBatchSystem') 619s DEBUG  toil.leader:leader.py:1455 Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v5 continues to exist (i.e. has more to do) 619s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v7 619s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-EncapsulatedJob/instance-8yqn9nyw" follows: 619s =========> 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'c8b78540-44ef-4d4f-b67e-7bdbf1a1adac', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': True, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmplo15ag5f', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/deferred/func3ipu26c2 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.worker] Parsed job description 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore'. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6) from description '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6) with ID (kind-EncapsulatedJob/instance-8yqn9nyw). 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6) with ID (kind-EncapsulatedJob/instance-8yqn9nyw) which wants 2147483648 of our 98062798848 bytes. 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98062798848 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98062798848 bytes 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:21+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 used 10.15x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:21+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 619s self.evaluatePromisedRequirements() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 619s ].getValue() 619s ~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 619s return func(*self._args) 619s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 619s 619s [2026-01-30T05:43:21+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [pydot] pydot initializing 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [pydot] pydot 4.0.1 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [pydot.core] pydot core module initializing 619s <========= 619s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v7 with ID kind-EncapsulatedJob/instance-8yqn9nyw to 0 619s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-8yqn9nyw', result_status=1) 619s DEBUG  toil.leader:leader.py:1620 Added job: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8 to updated jobs 619s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s DEBUG  toil.leader:leader.py:606 Updating status of job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8 with result status: 1 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-8yqn9nyw') 619s DEBUG  toil.leader:leader.py:1735 Found new failed successors: kind-Job/instance-k81ojz2c of job: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8 619s DEBUG  toil.leader:leader.py:1779 Totally failed job: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8 is marking direct predecessor: '_writer' kind-_writer/instance-yk1rpfbw v4 as having failed jobs 619s DEBUG  toil.leader:leader.py:1846 Cleaning the predecessors of kind-EncapsulatedJob/instance-8yqn9nyw 619s DEBUG  toil.toilState:toilState.py:283 Successors: one fewer for kind-_writer/instance-yk1rpfbw, now have 0 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-yk1rpfbw', result_status=0) 619s WARNING  toil.leader:leader.py:643 Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8 is completely failed 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:43:22: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 619s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:43:22: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 used 10.15x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-yk1rpfbw v4 with result status: 0 619s DEBUG  toil.leader:leader.py:597 Job kind-_writer/instance-yk1rpfbw is being processed as completely failed 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_writer', job_id='kind-_writer/instance-yk1rpfbw') 619s DEBUG  toil.leader:leader.py:1735 Found new failed successors: of job: '_writer' kind-_writer/instance-yk1rpfbw v4 619s DEBUG  toil.leader:leader.py:969 Finished the main loop: no jobs left to run. 619s DEBUG  toil.serviceManager:serviceManager.py:236 Waiting for service manager thread to finish ... 619s DEBUG  toil.serviceManager:serviceManager.py:261 Received signal to quit starting services. 619s DEBUG  toil.serviceManager:serviceManager.py:243 ... finished shutting down the service manager. Took 1.1180410385131836 seconds 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:296 Waiting for stats and logging collator thread to finish ... 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:300 ... finished collating stats and logs. Took 0.006304025650024414 seconds 619s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 619s INFO  toil.leader:leader.py:317 Finished toil run with 2 failed jobs. 619s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8 '_writer' kind-_writer/instance-yk1rpfbw v4 619s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 619s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 619s DEBUG  toil.common:common.py:1800 Shutting down batch system ... 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:317 Daddy thread cleaning up 0 remaining children for batch system 247544560384032... 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:325 Daddy thread for batch system 247544560384032 finishing because no children should now exist 619s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:503 Attempting worker cleanup 619s DEBUG  toil.lib.threading:threading.py:109 Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s DEBUG  toil.deferred:deferred.py:215 Cleaning up deferred functions system 619s DEBUG  toil.deferred:deferred.py:159 Opened with own state file /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/deferred/funcbbx1ay_k 619s DEBUG  toil.deferred:deferred.py:291 Running orphaned deferred functions 619s DEBUG  toil.deferred:deferred.py:369 Ran orphaned deferred functions from 0 abandoned state files 619s DEBUG  toil.deferred:deferred.py:167 Removing own state file /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/deferred/funcbbx1ay_k 619s DEBUG  toil.lib.threading:threading.py:109 Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s DEBUG  toil.fileStores.cachingFileStore:cachingFileStore.py:2402 Connecting to latest caching database cache-0.db for cleanup 619s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:517 Deleting workflow directory /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b 619s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:521 Deleting coordination directory /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b 619s DEBUG  toil.common:common.py:1802 ... finished shutting down the batch system in 0.014912128448486328 seconds. 619s INFO  toil.lib.history:history.py:530 Workflow c8b78540-44ef-4d4f-b67e-7bdbf1a1adac stopped. Success: False 619s __ TestSingleMachinePromisedRequirements.testPromisesWithNonCachingFileStore ___ 619s [gw0] linux -- Python 3.14.2 /usr/bin/python3.14 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 619s result: TResult | None = func() 619s ~~~~^^ 619s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 619s lambda: runtest_hook(item=item, **kwds), 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 619s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 619s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 619s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 619s raise exception 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 619s yield 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 619s return (yield) 619s ^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 619s return result.get_result() 619s ~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 619s raise exc.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 619s res = yield 619s ^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 619s teardown.throw(exception) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 619s return (yield) 619s ^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 619s res = hook_impl.function(*args) 619s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 619s item.runtest() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 619s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 619s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 619s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 619s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 619s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 619s raise exception 619s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 619s res = hook_impl.function(*args) 619s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 619s result = testfunction(**testargs) 619s File "/usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py", line 148, in testPromisesWithNonCachingFileStore 619s self.testPromisesWithJobStoreFileObjects(tmp_path, caching=False) 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py", line 145, in testPromisesWithJobStoreFileObjects 619s Job.Runner.startToil(F1, self.getOptions(tmp_path, caching=caching)) 619s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 619s return toil.start(job) 619s ~~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 619s return self._runMainLoop(rootJobDescription) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 619s ).run() 619s ~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 619s raise FailedJobsException( 619s ...<3 lines>... 619s ) 619s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore' contains 2 failed jobs: '_writer' kind-_writer/instance-lblqlima v4, '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8 619s Log from job "'_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8" follows: 619s =========> 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '224f5500-e669-4936-8dfe-2cd58050a1dc', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmp64rjpwws', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428/deferred/funchi7kmzyz 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.worker] Parsed job description 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore'. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6) from description '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:30+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 used 7.38x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:30+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 619s self.evaluatePromisedRequirements() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 619s ].getValue() 619s ~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 619s return func(*self._args) 619s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 619s 619s [2026-01-30T05:43:30+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [pydot] pydot initializing 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [pydot] pydot 4.0.1 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [pydot.core] pydot core module initializing 619s <========= 619s ----------------------------- Captured stderr call ----------------------------- 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.common] Initialized default configuration: {"config_version": 1.0} 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.batchSystems.options] Add options for aws_batch batch system 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.batchSystems.options] Add options for single_machine batch system 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.batchSystems.options] Add options for grid_engine batch system 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.batchSystems.options] Add options for lsf batch system 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.batchSystems.options] Add options for slurm batch system 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.batchSystems.options] Add options for torque batch system 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'asyncio', 'cachecontrol', 'concurrent', 'boto', 'humanfriendly', 'test', 'rdflib', 'salad', 'requests', 'werkzeug', 'debugWorkflow', 'botocore', 'urllib3', 'boto3', 'cwltest', 'docker', 'dill', 'bcdocs'} 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.statsAndLogging] Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'asyncio', 'cachecontrol', 'concurrent', 'boto', 'humanfriendly', 'test', 'rdflib', 'salad', 'requests', 'werkzeug', 'debugWorkflow', 'botocore', 'urllib3', 'boto3', 'cwltest', 'docker', 'dill', 'bcdocs'} 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.statsAndLogging] Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.common] Initialized default configuration: {"config_version": 1.0} 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.batchSystems.options] Add options for aws_batch batch system 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.batchSystems.options] Add options for single_machine batch system 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.batchSystems.options] Add options for grid_engine batch system 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.batchSystems.options] Add options for lsf batch system 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.batchSystems.options] Add options for slurm batch system 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.batchSystems.options] Add options for torque batch system 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.common] Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': None, 'logRotating': False, 'colored_logs': True, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'onSuccess', 'cleanWorkDir': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'coalesceStatusCalls': True, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'memory_is_product': False, 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'symlinkImports': True, 'moveOutputs': False, 'caching': False, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'maxNodes': [10], 'minNodes': [0], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'metrics': False, 'assume_zero_overhead': False, 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': False, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, 'publish_workflow_metrics': None, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'linkImports': None, 'moveExports': None, 'enableCaching': None, 'not_strict': False, 'enable_dev': False, 'enable_ext': False, 'quiet': False, 'basedir': None, 'outdir': None, 'log_dir': '', 'user_space_docker_cmd': None, 'singularity': False, 'podman': False, 'no_container': False, 'rm_container': True, 'custom_net': None, 'record_container_id': False, 'cidfile_dir': None, 'cidfile_prefix': None, 'no_prepull': False, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'beta_dependency_resolvers_configuration': None, 'beta_dependencies_directory': None, 'beta_use_biocontainers': None, 'beta_conda_dependencies': None, 'tmpdir_prefix': None, 'tmp_outdir_prefix': None, 'force_docker_pull': False, 'no_match_user': False, 'no_read_only': False, 'strict_memory_limit': False, 'strict_cpu_limit': False, 'relax_path_checks': False, 'default_container': None, 'do_validate': True, 'fast_parser': False, 'compute_checksum': True, 'eval_timeout': 20, 'overrides': None, 'mpi_config_file': None, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'cwl_default_ram': True, 'cwl_min_ram': None, 'destBucket': None, 'cachedir': None, 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto', 'all_call_outputs': None, 'strict': False, 'quant_check': True, 'run_imports_on_workers': False, 'import_workers_batchsize': 1073741824, 'import_workers_disk': 1048576} 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore'. 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.jobStores.abstractJobStore] The workflow ID is: '224f5500-e669-4936-8dfe-2cd58050a1dc' 619s [2026-01-30T05:43:27+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 224f5500-e669-4936-8dfe-2cd58050a1dc in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore 619s [2026-01-30T05:43:27+0000] [MainThread] [I] [toil.lib.history] Workflow 224f5500-e669-4936-8dfe-2cd58050a1dc is a run of 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.common] Using the single machine batch system 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.common] Created the workflow directory for this machine at /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir/toilwf-1342b098ef205e0295f50d1d5c0c1428 619s [2026-01-30T05:43:27+0000] [Thread-99 (daddy)] [D] [toil.batchSystems.singleMachine] Started daddy thread for batch system 247544572107376. 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Started batch system 247544572107376 in normal mode. 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.common] User script ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.common] No user script to auto-deploy. 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.common] Written the environment for the jobs to the environment file 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.common] Caching all jobs in job store 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.common] 0 jobs downloaded. 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-47efe6481c6444a88d70e9411f265eb8/stream for result of '_writer' TemporaryID(8eb4b10f-edd8-4b2e-8862-8da03cca81cf) v0 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.job] Saving graph of 5 jobs, 5 non-service, 5 new 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.job] Processing job 'Job' kind-Job/instance-nyw4dxoy v0 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.job] Processing job '_follower' kind-_follower/instance-v6ahb0pj v0 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-bfa948d9b7a14750868c931170f2ce4a/stream for result of '_writer' kind-_writer/instance-lblqlima v0 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-688577d1a9064b309730608c69d4cdef/stream for result of '_writer' kind-_writer/instance-03cwumjk v0 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v0 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-03cwumjk v0 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-lblqlima v0 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.job] New job version: 'Job' kind-Job/instance-nyw4dxoy v1 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-_follower/instance-v6ahb0pj v1 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-03cwumjk v1 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-lblqlima v1 619s [2026-01-30T05:43:27+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '224f5500-e669-4936-8dfe-2cd58050a1dc', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmp64rjpwws', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:27+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.bus] Listening for message topic: toil.bus.JobUpdatedMessage 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.toilState] Found job to run: kind-_writer/instance-lblqlima, with body: True, with checkpoint: False, with services: False, with no next successors: False 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-lblqlima', result_status=0) 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.leader] Found 1 jobs to start and 0 jobs with successors to run 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.leader] Checked batch system has no running jobs and no updated jobs 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.serviceManager] Initializing service manager 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-lblqlima v1 with result status: 0 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore kind-_writer/instance-lblqlima with disk: 2.0 Gi, memory: 2.0 Gi, cores: 2.0, accelerators: [], preemptible: False 619s [2026-01-30T05:43:27+0000] [MainThread] [I] [toil.leader] Issued job '_writer' kind-_writer/instance-lblqlima v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 2, accelerators: [], preemptible: False 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_writer', job_id='kind-_writer/instance-lblqlima', toil_batch_id=1) 619s [2026-01-30T05:43:27+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 619s [2026-01-30T05:43:27+0000] [Thread-99 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore kind-_writer/instance-lblqlima 619s [2026-01-30T05:43:27+0000] [Thread-99 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 1 as child 10503 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'requests', 'concurrent', 'botocore', 'boto3', 'urllib3', 'boto', 'docker', 'dill', 'asyncio'} 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.worker] Worker started for job _writer... 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.common] Obtained node ID d997a28e7a334b4298ab4a55574a1a13 from file /var/lib/dbus/machine-id 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir/toilwf-1342b098ef205e0295f50d1d5c0c1428/d232/worker_log.txt 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428/deferred/funcb0m8cich 619s [2026-01-30T05:43:28+0000] [Thread-99 (daddy)] [D] [toil.batchSystems.singleMachine] Child 10503 for job 1 succeeded 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 1 with exit value: 0 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.leader] Job ended: '_writer' kind-_writer/instance-lblqlima v1 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_writer', job_id='kind-_writer/instance-lblqlima', exit_code=0) 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=1, external_batch_id='10503', batch_system='SingleMachineBatchSystem') 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.leader] Job '_writer' kind-_writer/instance-lblqlima v1 continues to exist (i.e. has more to do) 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-lblqlima', result_status=0) 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.leader] Added job: '_writer' kind-_writer/instance-lblqlima v4 to updated jobs 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-lblqlima v4 with result status: 0 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.leader] Job: kind-_writer/instance-lblqlima has 1 successors to schedule 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.toilState] Successors: 1 more for kind-_writer/instance-lblqlima, now have 1 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.leader] Added job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 as coming after job '_writer' kind-_writer/instance-lblqlima v4 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-0vvnaeqh with disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.leader] Issued job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 with job batch system ID: 2 and disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-0vvnaeqh', toil_batch_id=2) 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 619s [2026-01-30T05:43:28+0000] [Thread-99 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-0vvnaeqh 619s [2026-01-30T05:43:28+0000] [Thread-99 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 2 as child 10524 619s [2026-01-30T05:43:28+0000] [Thread-102 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:43:28: Job '_writer' kind-_writer/instance-lblqlima v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:28+0000] [Thread-102 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:43:28: Job '_writer' kind-_writer/instance-lblqlima v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:28+0000] [Thread-102 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Received Toil worker log. Disable debug level logging to hide this output 619s [2026-01-30T05:43:28+0000] [Thread-102 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Log from job "JobFunctionWrappingJob" follows: 619s =========> 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '224f5500-e669-4936-8dfe-2cd58050a1dc', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmp64rjpwws', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428/deferred/funcb0m8cich 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.worker] Parsed job description 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-lblqlima v1 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-lblqlima v1) from description '_writer' kind-_writer/instance-lblqlima v1 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Loading user function _writer from module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-47efe6481c6444a88d70e9411f265eb8/stream from Job('_writer' kind-_writer/instance-lblqlima v1) with a 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-bfa948d9b7a14750868c931170f2ce4a/stream from Job('_writer' kind-_writer/instance-lblqlima v1) with a 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-lblqlima v1 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-lblqlima v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-lblqlima v2 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-lblqlima v2 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-lblqlima v2 would chain to ID kind-_writer/instance-03cwumjk 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Chaining from '_writer' kind-_writer/instance-lblqlima v2 to '_writer' kind-_writer/instance-03cwumjk v1 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] '_writer' kind-_writer/instance-03cwumjk v1 is adopting successor phases from '_writer' kind-_writer/instance-lblqlima v2 of: [] 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-lblqlima v3 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.worker] Starting the next job 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-lblqlima v3 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-lblqlima v3) from description '_writer' kind-_writer/instance-lblqlima v3 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Loading user function _writer from module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-688577d1a9064b309730608c69d4cdef/stream from Job('_writer' kind-_writer/instance-lblqlima v3) with a 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-lblqlima v3 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-lblqlima v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-lblqlima v4 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-lblqlima v4 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-lblqlima v4 would chain to ID kind-EncapsulatedJob/instance-0vvnaeqh 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.worker] Preemptibility is different for the next job, returning to the leader 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Not chaining from job '_writer' kind-_writer/instance-lblqlima v4 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir/toilwf-1342b098ef205e0295f50d1d5c0c1428/d232. Set --cleanWorkDir to retain this log 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 0.317750 seconds 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [pydot] pydot initializing 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [pydot] pydot 4.0.1 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [pydot.core] pydot core module initializing 619s <========= 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'botocore', 'dill', 'boto3', 'requests', 'asyncio', 'boto', 'urllib3', 'concurrent', 'docker'} 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.worker] Worker started for job EncapsulatedJob... 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.common] Obtained node ID d997a28e7a334b4298ab4a55574a1a13 from file /var/lib/dbus/machine-id 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir/toilwf-1342b098ef205e0295f50d1d5c0c1428/f3b3/worker_log.txt 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v4 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428/deferred/funck24y8gqe 619s [2026-01-30T05:43:29+0000] [Thread-99 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-0vvnaeqh. 619s [2026-01-30T05:43:29+0000] [Thread-99 (daddy)] [D] [toil.batchSystems.singleMachine] Child 10524 for job 2 succeeded 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 2 with exit value: 1 619s [2026-01-30T05:43:29+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 619s Exit reason: None 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-0vvnaeqh', exit_code=1) 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=2, external_batch_id='10524', batch_system='SingleMachineBatchSystem') 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.leader] Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 continues to exist (i.e. has more to do) 619s [2026-01-30T05:43:29+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v4 619s [2026-01-30T05:43:29+0000] [MainThread] [W] [toil.leader] Log from job "kind-EncapsulatedJob/instance-0vvnaeqh" follows: 619s =========> 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '224f5500-e669-4936-8dfe-2cd58050a1dc', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmp64rjpwws', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428/deferred/funck24y8gqe 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.worker] Parsed job description 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] Working on job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] Loaded body Job('EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1) from description 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v2 619s [2026-01-30T05:43:29+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v2 used 10.33x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] Completed body for 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v2 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.worker] 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v2 would chain to ID kind-_follower/instance-v6ahb0pj 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] Chaining from 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v2 to '_follower' kind-_follower/instance-v6ahb0pj v1 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] '_follower' kind-_follower/instance-v6ahb0pj v1 is adopting successor phases from 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v2 of: [{'kind-Job/instance-nyw4dxoy'}] 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v3 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.worker] Starting the next job 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v3 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore'. 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-0vvnaeqh v3) from description '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v3 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:29+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v3 used 9.97x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:29+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 619s self.evaluatePromisedRequirements() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 619s ].getValue() 619s ~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 619s return func(*self._args) 619s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 619s 619s [2026-01-30T05:43:29+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [pydot] pydot initializing 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [pydot] pydot 4.0.1 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [pydot.core] pydot core module initializing 619s <========= 619s [2026-01-30T05:43:29+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v4 with ID kind-EncapsulatedJob/instance-0vvnaeqh to 1 619s [2026-01-30T05:43:29+0000] [MainThread] [W] [toil.job] We have increased the default memory of the failed job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v4 to 2147483648 bytes 619s [2026-01-30T05:43:29+0000] [MainThread] [W] [toil.job] We have increased the disk of the failed job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v4 to the default of 2147483648 bytes 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v5 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-0vvnaeqh', result_status=1) 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.leader] Added job: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v5 to updated jobs 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.leader] Updating status of job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v5 with result status: 1 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-0vvnaeqh with disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.leader] Issued job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v5 with job batch system ID: 3 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-0vvnaeqh', toil_batch_id=3) 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 619s [2026-01-30T05:43:29+0000] [Thread-99 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-0vvnaeqh 619s [2026-01-30T05:43:29+0000] [Thread-99 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 3 as child 10570 619s [2026-01-30T05:43:29+0000] [Thread-102 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:43:29: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 619s [2026-01-30T05:43:29+0000] [Thread-102 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:43:29: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v2 used 10.33x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:29+0000] [Thread-102 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:43:29: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 619s [2026-01-30T05:43:29+0000] [Thread-102 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:43:29: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v3 used 9.97x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'botocore', 'docker', 'boto', 'urllib3', 'boto3', 'dill', 'asyncio', 'requests', 'concurrent'} 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.worker] Worker started for job _follower... 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.common] Obtained node ID d997a28e7a334b4298ab4a55574a1a13 from file /var/lib/dbus/machine-id 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir/toilwf-1342b098ef205e0295f50d1d5c0c1428/4abb/worker_log.txt 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v7 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428/deferred/funchi7kmzyz 619s [2026-01-30T05:43:30+0000] [Thread-99 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-0vvnaeqh. 619s [2026-01-30T05:43:30+0000] [Thread-99 (daddy)] [D] [toil.batchSystems.singleMachine] Child 10570 for job 3 succeeded 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 3 with exit value: 1 619s [2026-01-30T05:43:30+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v5 619s Exit reason: None 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-0vvnaeqh', exit_code=1) 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=3, external_batch_id='10570', batch_system='SingleMachineBatchSystem') 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.leader] Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v5 continues to exist (i.e. has more to do) 619s [2026-01-30T05:43:30+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v7 619s [2026-01-30T05:43:30+0000] [MainThread] [W] [toil.leader] Log from job "kind-EncapsulatedJob/instance-0vvnaeqh" follows: 619s =========> 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '224f5500-e669-4936-8dfe-2cd58050a1dc', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmp64rjpwws', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428/deferred/funchi7kmzyz 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.worker] Parsed job description 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore'. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6) from description '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:30+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 used 7.38x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:30+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 619s self.evaluatePromisedRequirements() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 619s ].getValue() 619s ~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 619s return func(*self._args) 619s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 619s 619s [2026-01-30T05:43:30+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [pydot] pydot initializing 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [pydot] pydot 4.0.1 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [pydot.core] pydot core module initializing 619s <========= 619s [2026-01-30T05:43:30+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v7 with ID kind-EncapsulatedJob/instance-0vvnaeqh to 0 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-0vvnaeqh', result_status=1) 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.leader] Added job: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8 to updated jobs 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.leader] Updating status of job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8 with result status: 1 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-0vvnaeqh') 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.leader] Found new failed successors: kind-Job/instance-nyw4dxoy of job: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.leader] Totally failed job: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8 is marking direct predecessor: '_writer' kind-_writer/instance-lblqlima v4 as having failed jobs 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.leader] Cleaning the predecessors of kind-EncapsulatedJob/instance-0vvnaeqh 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.toilState] Successors: one fewer for kind-_writer/instance-lblqlima, now have 0 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-lblqlima', result_status=0) 619s [2026-01-30T05:43:30+0000] [MainThread] [W] [toil.leader] Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8 is completely failed 619s [2026-01-30T05:43:30+0000] [Thread-102 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:43:30: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:30+0000] [Thread-102 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:43:30: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 used 7.38x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:32+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s [2026-01-30T05:43:32+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-lblqlima v4 with result status: 0 619s [2026-01-30T05:43:32+0000] [MainThread] [D] [toil.leader] Job kind-_writer/instance-lblqlima is being processed as completely failed 619s [2026-01-30T05:43:32+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_writer', job_id='kind-_writer/instance-lblqlima') 619s [2026-01-30T05:43:32+0000] [MainThread] [D] [toil.leader] Found new failed successors: of job: '_writer' kind-_writer/instance-lblqlima v4 619s [2026-01-30T05:43:34+0000] [MainThread] [D] [toil.leader] Finished the main loop: no jobs left to run. 619s [2026-01-30T05:43:34+0000] [MainThread] [D] [toil.serviceManager] Waiting for service manager thread to finish ... 619s [2026-01-30T05:43:34+0000] [Thread-101 (__start_services)] [D] [toil.serviceManager] Received signal to quit starting services. 619s [2026-01-30T05:43:35+0000] [MainThread] [D] [toil.serviceManager] ... finished shutting down the service manager. Took 1.2462890148162842 seconds 619s [2026-01-30T05:43:35+0000] [MainThread] [D] [toil.statsAndLogging] Waiting for stats and logging collator thread to finish ... 619s [2026-01-30T05:43:35+0000] [MainThread] [D] [toil.statsAndLogging] ... finished collating stats and logs. Took 0.00667119026184082 seconds 619s [2026-01-30T05:43:35+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 619s [2026-01-30T05:43:35+0000] [MainThread] [I] [toil.leader] Finished toil run with 2 failed jobs. 619s [2026-01-30T05:43:35+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_writer' kind-_writer/instance-lblqlima v4 '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8 619s [2026-01-30T05:43:35+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 619s [2026-01-30T05:43:36+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 619s [2026-01-30T05:43:36+0000] [MainThread] [D] [toil.common] Shutting down batch system ... 619s [2026-01-30T05:43:36+0000] [Thread-99 (daddy)] [D] [toil.batchSystems.singleMachine] Daddy thread cleaning up 0 remaining children for batch system 247544572107376... 619s [2026-01-30T05:43:36+0000] [Thread-99 (daddy)] [D] [toil.batchSystems.singleMachine] Daddy thread for batch system 247544572107376 finishing because no children should now exist 619s [2026-01-30T05:43:36+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Attempting worker cleanup 619s [2026-01-30T05:43:36+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:36+0000] [MainThread] [D] [toil.deferred] Cleaning up deferred functions system 619s [2026-01-30T05:43:36+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428/deferred/func39m8f9uo 619s [2026-01-30T05:43:36+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:36+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:36+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428/deferred/func39m8f9uo 619s [2026-01-30T05:43:36+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:36+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Deleting workflow directory /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir/toilwf-1342b098ef205e0295f50d1d5c0c1428 619s [2026-01-30T05:43:36+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Deleting coordination directory /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 619s [2026-01-30T05:43:36+0000] [MainThread] [D] [toil.common] ... finished shutting down the batch system in 0.012995243072509766 seconds. 619s [2026-01-30T05:43:36+0000] [MainThread] [I] [toil.lib.history] Workflow 224f5500-e669-4936-8dfe-2cd58050a1dc stopped. Success: False 619s ------------------------------ Captured log call ------------------------------- 619s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s DEBUG  toil.common:common.py:796 Initialized default configuration: {"config_version": 1.0} 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for aws_batch batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for single_machine batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for grid_engine batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for lsf batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for slurm batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for torque batch system 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:488 Suppressing the following loggers: {'asyncio', 'cachecontrol', 'concurrent', 'boto', 'humanfriendly', 'test', 'rdflib', 'salad', 'requests', 'werkzeug', 'debugWorkflow', 'botocore', 'urllib3', 'boto3', 'cwltest', 'docker', 'dill', 'bcdocs'} 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:447 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:488 Suppressing the following loggers: {'asyncio', 'cachecontrol', 'concurrent', 'boto', 'humanfriendly', 'test', 'rdflib', 'salad', 'requests', 'werkzeug', 'debugWorkflow', 'botocore', 'urllib3', 'boto3', 'cwltest', 'docker', 'dill', 'bcdocs'} 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:447 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 619s DEBUG  toil.common:common.py:796 Initialized default configuration: {"config_version": 1.0} 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for aws_batch batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for single_machine batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for grid_engine batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for lsf batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for slurm batch system 619s DEBUG  toil.batchSystems.options:options.py:207 Add options for torque batch system 619s DEBUG  toil.common:common.py:1006 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': None, 'logRotating': False, 'colored_logs': True, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'onSuccess', 'cleanWorkDir': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'coalesceStatusCalls': True, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'memory_is_product': False, 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'symlinkImports': True, 'moveOutputs': False, 'caching': False, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'maxNodes': [10], 'minNodes': [0], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'metrics': False, 'assume_zero_overhead': False, 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': False, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, 'publish_workflow_metrics': None, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'linkImports': None, 'moveExports': None, 'enableCaching': None, 'not_strict': False, 'enable_dev': False, 'enable_ext': False, 'quiet': False, 'basedir': None, 'outdir': None, 'log_dir': '', 'user_space_docker_cmd': None, 'singularity': False, 'podman': False, 'no_container': False, 'rm_container': True, 'custom_net': None, 'record_container_id': False, 'cidfile_dir': None, 'cidfile_prefix': None, 'no_prepull': False, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'beta_dependency_resolvers_configuration': None, 'beta_dependencies_directory': None, 'beta_use_biocontainers': None, 'beta_conda_dependencies': None, 'tmpdir_prefix': None, 'tmp_outdir_prefix': None, 'force_docker_pull': False, 'no_match_user': False, 'no_read_only': False, 'strict_memory_limit': False, 'strict_cpu_limit': False, 'relax_path_checks': False, 'default_container': None, 'do_validate': True, 'fast_parser': False, 'compute_checksum': True, 'eval_timeout': 20, 'overrides': None, 'mpi_config_file': None, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'cwl_default_ram': True, 'cwl_min_ram': None, 'destBucket': None, 'cachedir': None, 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto', 'all_call_outputs': None, 'strict': False, 'quant_check': True, 'run_imports_on_workers': False, 'import_workers_batchsize': 1073741824, 'import_workers_disk': 1048576} 619s DEBUG  toil.jobStores.fileJobStore:fileJobStore.py:93 Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore'. 619s DEBUG  toil.jobStores.abstractJobStore:abstractJobStore.py:212 The workflow ID is: '224f5500-e669-4936-8dfe-2cd58050a1dc' 619s INFO  toil.lib.history:history.py:369 Recording workflow creation of 224f5500-e669-4936-8dfe-2cd58050a1dc in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore 619s INFO  toil.lib.history:history.py:399 Workflow 224f5500-e669-4936-8dfe-2cd58050a1dc is a run of 619s DEBUG  toil.common:common.py:1346 Using the single machine batch system 619s DEBUG  toil.common:common.py:1723 Created the workflow directory for this machine at /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir/toilwf-1342b098ef205e0295f50d1d5c0c1428 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:247 Started daddy thread for batch system 247544572107376. 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:229 Started batch system 247544572107376 in normal mode. 619s DEBUG  toil.common:common.py:1367 User script ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. 619s DEBUG  toil.common:common.py:1409 No user script to auto-deploy. 619s DEBUG  toil.common:common.py:1576 Written the environment for the jobs to the environment file 619s DEBUG  toil.common:common.py:1580 Caching all jobs in job store 619s DEBUG  toil.common:common.py:1584 0 jobs downloaded. 619s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-47efe6481c6444a88d70e9411f265eb8/stream for result of '_writer' TemporaryID(8eb4b10f-edd8-4b2e-8862-8da03cca81cf) v0 619s DEBUG  toil.job:job.py:3000 Saving graph of 5 jobs, 5 non-service, 5 new 619s DEBUG  toil.job:job.py:3023 Processing job 'Job' kind-Job/instance-nyw4dxoy v0 619s DEBUG  toil.job:job.py:3023 Processing job '_follower' kind-_follower/instance-v6ahb0pj v0 619s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-bfa948d9b7a14750868c931170f2ce4a/stream for result of '_writer' kind-_writer/instance-lblqlima v0 619s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-688577d1a9064b309730608c69d4cdef/stream for result of '_writer' kind-_writer/instance-03cwumjk v0 619s DEBUG  toil.job:job.py:3023 Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v0 619s DEBUG  toil.job:job.py:3023 Processing job '_writer' kind-_writer/instance-03cwumjk v0 619s DEBUG  toil.job:job.py:3023 Processing job '_writer' kind-_writer/instance-lblqlima v0 619s DEBUG  toil.job:job.py:1507 New job version: 'Job' kind-Job/instance-nyw4dxoy v1 619s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-_follower/instance-v6ahb0pj v1 619s DEBUG  toil.job:job.py:1507 New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 619s DEBUG  toil.job:job.py:1507 New job version: '_writer' kind-_writer/instance-03cwumjk v1 619s DEBUG  toil.job:job.py:1507 New job version: '_writer' kind-_writer/instance-lblqlima v1 619s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s DEBUG  toil:__init__.py:481 Configuration: {'cwl': False, 'workflowID': '224f5500-e669-4936-8dfe-2cd58050a1dc', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmp64rjpwws', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 619s DEBUG  toil.bus:bus.py:403 Listening for message topic: toil.bus.JobUpdatedMessage 619s DEBUG  toil.toilState:toilState.py:322 Found job to run: kind-_writer/instance-lblqlima, with body: True, with checkpoint: False, with services: False, with no next successors: False 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-lblqlima', result_status=0) 619s DEBUG  toil.leader:leader.py:145 Found 1 jobs to start and 0 jobs with successors to run 619s DEBUG  toil.leader:leader.py:157 Checked batch system has no running jobs and no updated jobs 619s DEBUG  toil.serviceManager:serviceManager.py:35 Initializing service manager 619s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-lblqlima v1 with result status: 0 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore kind-_writer/instance-lblqlima with disk: 2.0 Gi, memory: 2.0 Gi, cores: 2.0, accelerators: [], preemptible: False 619s INFO  toil.leader:leader.py:1132 Issued job '_writer' kind-_writer/instance-lblqlima v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 2, accelerators: [], preemptible: False 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_writer', job_id='kind-_writer/instance-lblqlima', toil_batch_id=1) 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore kind-_writer/instance-lblqlima 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 1 as child 10503 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 10503 for job 1 succeeded 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 1 with exit value: 0 619s DEBUG  toil.leader:leader.py:846 Job ended: '_writer' kind-_writer/instance-lblqlima v1 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_writer', job_id='kind-_writer/instance-lblqlima', exit_code=0) 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=1, external_batch_id='10503', batch_system='SingleMachineBatchSystem') 619s DEBUG  toil.leader:leader.py:1455 Job '_writer' kind-_writer/instance-lblqlima v1 continues to exist (i.e. has more to do) 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-lblqlima', result_status=0) 619s DEBUG  toil.leader:leader.py:1620 Added job: '_writer' kind-_writer/instance-lblqlima v4 to updated jobs 619s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 619s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-lblqlima v4 with result status: 0 619s DEBUG  toil.leader:leader.py:506 Job: kind-_writer/instance-lblqlima has 1 successors to schedule 619s DEBUG  toil.toilState:toilState.py:264 Successors: 1 more for kind-_writer/instance-lblqlima, now have 1 619s DEBUG  toil.leader:leader.py:476 Added job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 as coming after job '_writer' kind-_writer/instance-lblqlima v4 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-0vvnaeqh with disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 619s INFO  toil.leader:leader.py:1132 Issued job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 with job batch system ID: 2 and disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-0vvnaeqh', toil_batch_id=2) 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-0vvnaeqh 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 2 as child 10524 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:43:28: Job '_writer' kind-_writer/instance-lblqlima v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:43:28: Job '_writer' kind-_writer/instance-lblqlima v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:98 Received Toil worker log. Disable debug level logging to hide this output 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:101 Log from job "JobFunctionWrappingJob" follows: 619s =========> 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '224f5500-e669-4936-8dfe-2cd58050a1dc', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmp64rjpwws', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428/deferred/funcb0m8cich 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.worker] Parsed job description 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-lblqlima v1 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-lblqlima v1) from description '_writer' kind-_writer/instance-lblqlima v1 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Loading user function _writer from module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-47efe6481c6444a88d70e9411f265eb8/stream from Job('_writer' kind-_writer/instance-lblqlima v1) with a 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-bfa948d9b7a14750868c931170f2ce4a/stream from Job('_writer' kind-_writer/instance-lblqlima v1) with a 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-lblqlima v1 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-lblqlima v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-lblqlima v2 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-lblqlima v2 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-lblqlima v2 would chain to ID kind-_writer/instance-03cwumjk 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Chaining from '_writer' kind-_writer/instance-lblqlima v2 to '_writer' kind-_writer/instance-03cwumjk v1 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] '_writer' kind-_writer/instance-03cwumjk v1 is adopting successor phases from '_writer' kind-_writer/instance-lblqlima v2 of: [] 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-lblqlima v3 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.worker] Starting the next job 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-lblqlima v3 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-lblqlima v3) from description '_writer' kind-_writer/instance-lblqlima v3 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Loading user function _writer from module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-688577d1a9064b309730608c69d4cdef/stream from Job('_writer' kind-_writer/instance-lblqlima v3) with a 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-lblqlima v3 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-lblqlima v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-lblqlima v4 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-lblqlima v4 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-lblqlima v4 would chain to ID kind-EncapsulatedJob/instance-0vvnaeqh 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [toil.worker] Preemptibility is different for the next job, returning to the leader 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Not chaining from job '_writer' kind-_writer/instance-lblqlima v4 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir/toilwf-1342b098ef205e0295f50d1d5c0c1428/d232. Set --cleanWorkDir to retain this log 619s [2026-01-30T05:43:28+0000] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 0.317750 seconds 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [pydot] pydot initializing 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [pydot] pydot 4.0.1 619s [2026-01-30T05:43:28+0000] [MainThread] [D] [pydot.core] pydot core module initializing 619s <========= 619s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-0vvnaeqh. 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 10524 for job 2 succeeded 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 2 with exit value: 1 619s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 619s Exit reason: None 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-0vvnaeqh', exit_code=1) 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=2, external_batch_id='10524', batch_system='SingleMachineBatchSystem') 619s DEBUG  toil.leader:leader.py:1455 Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 continues to exist (i.e. has more to do) 619s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v4 619s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-EncapsulatedJob/instance-0vvnaeqh" follows: 619s =========> 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '224f5500-e669-4936-8dfe-2cd58050a1dc', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmp64rjpwws', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428/deferred/funck24y8gqe 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.worker] Parsed job description 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] Working on job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] Loaded body Job('EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1) from description 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v2 619s [2026-01-30T05:43:29+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v2 used 10.33x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] Completed body for 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v2 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.worker] 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v2 would chain to ID kind-_follower/instance-v6ahb0pj 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] Chaining from 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v2 to '_follower' kind-_follower/instance-v6ahb0pj v1 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] '_follower' kind-_follower/instance-v6ahb0pj v1 is adopting successor phases from 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v2 of: [{'kind-Job/instance-nyw4dxoy'}] 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v3 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.worker] Starting the next job 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v3 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore'. 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-0vvnaeqh v3) from description '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v3 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:29+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v3 used 9.97x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:29+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 619s self.evaluatePromisedRequirements() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 619s ].getValue() 619s ~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 619s return func(*self._args) 619s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 619s 619s [2026-01-30T05:43:29+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [pydot] pydot initializing 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [pydot] pydot 4.0.1 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [pydot.core] pydot core module initializing 619s <========= 619s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v4 with ID kind-EncapsulatedJob/instance-0vvnaeqh to 1 619s WARNING  toil.job:job.py:1413 We have increased the default memory of the failed job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v4 to 2147483648 bytes 619s WARNING  toil.job:job.py:1421 We have increased the disk of the failed job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v4 to the default of 2147483648 bytes 619s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v5 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-0vvnaeqh', result_status=1) 619s DEBUG  toil.leader:leader.py:1620 Added job: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v5 to updated jobs 619s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s DEBUG  toil.leader:leader.py:606 Updating status of job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v5 with result status: 1 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-0vvnaeqh with disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 619s INFO  toil.leader:leader.py:1132 Issued job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v5 with job batch system ID: 3 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-0vvnaeqh', toil_batch_id=3) 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-0vvnaeqh 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 3 as child 10570 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:43:29: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 619s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:43:29: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-0vvnaeqh v2 used 10.33x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:43:29: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 619s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:43:29: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v3 used 9.97x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-0vvnaeqh. 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 10570 for job 3 succeeded 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 3 with exit value: 1 619s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v5 619s Exit reason: None 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-0vvnaeqh', exit_code=1) 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=3, external_batch_id='10570', batch_system='SingleMachineBatchSystem') 619s DEBUG  toil.leader:leader.py:1455 Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v5 continues to exist (i.e. has more to do) 619s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v7 619s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-EncapsulatedJob/instance-0vvnaeqh" follows: 619s =========> 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '224f5500-e669-4936-8dfe-2cd58050a1dc', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmp64rjpwws', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428/deferred/funchi7kmzyz 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.worker] Parsed job description 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore'. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6) from description '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:30+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 used 7.38x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:30+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 619s self.evaluatePromisedRequirements() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 619s ].getValue() 619s ~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 619s return func(*self._args) 619s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 619s 619s [2026-01-30T05:43:30+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [pydot] pydot initializing 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [pydot] pydot 4.0.1 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [pydot.core] pydot core module initializing 619s <========= 619s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v7 with ID kind-EncapsulatedJob/instance-0vvnaeqh to 0 619s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-0vvnaeqh', result_status=1) 619s DEBUG  toil.leader:leader.py:1620 Added job: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8 to updated jobs 619s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s DEBUG  toil.leader:leader.py:606 Updating status of job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8 with result status: 1 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-0vvnaeqh') 619s DEBUG  toil.leader:leader.py:1735 Found new failed successors: kind-Job/instance-nyw4dxoy of job: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8 619s DEBUG  toil.leader:leader.py:1779 Totally failed job: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8 is marking direct predecessor: '_writer' kind-_writer/instance-lblqlima v4 as having failed jobs 619s DEBUG  toil.leader:leader.py:1846 Cleaning the predecessors of kind-EncapsulatedJob/instance-0vvnaeqh 619s DEBUG  toil.toilState:toilState.py:283 Successors: one fewer for kind-_writer/instance-lblqlima, now have 0 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-lblqlima', result_status=0) 619s WARNING  toil.leader:leader.py:643 Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8 is completely failed 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:43:30: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 619s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:43:30: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 used 7.38x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 619s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-lblqlima v4 with result status: 0 619s DEBUG  toil.leader:leader.py:597 Job kind-_writer/instance-lblqlima is being processed as completely failed 619s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_writer', job_id='kind-_writer/instance-lblqlima') 619s DEBUG  toil.leader:leader.py:1735 Found new failed successors: of job: '_writer' kind-_writer/instance-lblqlima v4 619s DEBUG  toil.leader:leader.py:969 Finished the main loop: no jobs left to run. 619s DEBUG  toil.serviceManager:serviceManager.py:236 Waiting for service manager thread to finish ... 619s DEBUG  toil.serviceManager:serviceManager.py:261 Received signal to quit starting services. 619s DEBUG  toil.serviceManager:serviceManager.py:243 ... finished shutting down the service manager. Took 1.2462890148162842 seconds 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:296 Waiting for stats and logging collator thread to finish ... 619s DEBUG  toil.statsAndLogging:statsAndLogging.py:300 ... finished collating stats and logs. Took 0.00667119026184082 seconds 619s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 619s INFO  toil.leader:leader.py:317 Finished toil run with 2 failed jobs. 619s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_writer' kind-_writer/instance-lblqlima v4 '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8 619s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 619s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 619s DEBUG  toil.common:common.py:1800 Shutting down batch system ... 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:317 Daddy thread cleaning up 0 remaining children for batch system 247544572107376... 619s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:325 Daddy thread for batch system 247544572107376 finishing because no children should now exist 619s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:503 Attempting worker cleanup 619s DEBUG  toil.lib.threading:threading.py:109 Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s DEBUG  toil.deferred:deferred.py:215 Cleaning up deferred functions system 619s DEBUG  toil.deferred:deferred.py:159 Opened with own state file /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428/deferred/func39m8f9uo 619s DEBUG  toil.deferred:deferred.py:291 Running orphaned deferred functions 619s DEBUG  toil.deferred:deferred.py:369 Ran orphaned deferred functions from 0 abandoned state files 619s DEBUG  toil.deferred:deferred.py:167 Removing own state file /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428/deferred/func39m8f9uo 619s DEBUG  toil.lib.threading:threading.py:109 Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:517 Deleting workflow directory /tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir/toilwf-1342b098ef205e0295f50d1d5c0c1428 619s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:521 Deleting coordination directory /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 619s DEBUG  toil.common:common.py:1802 ... finished shutting down the batch system in 0.012995243072509766 seconds. 619s INFO  toil.lib.history:history.py:530 Workflow 224f5500-e669-4936-8dfe-2cd58050a1dc stopped. Success: False 619s =========================== short test summary info ============================ 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:603: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:603: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:217: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:217: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:189: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:189: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1115: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1127: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1115: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1127: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:621: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:621: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:825: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:825: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:800: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:151: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:800: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:160: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:151: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:313: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:160: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:202: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1467: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1446: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:313: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1079: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:202: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:450: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:238: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1079: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:421: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:405: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:450: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:238: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:380: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:529: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:421: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:264: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:405: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:585: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:960: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:380: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [13] ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py:1139: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:529: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:264: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:585: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:960: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [13] ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py:1139: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:32: Consumes unauthenticated Docker Hub pulls if run 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:38: Consumes unauthenticated Docker Hub pulls if run 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:45: Consumes unauthenticated Docker Hub pulls if run 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:26: Consumes unauthenticated Docker Hub pulls if run 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:731: Install Toil with the 'server' extra to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:646: Install Toil with the 'server' extra to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:697: Install Toil with the 'server' extra to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:706: Install Toil with the 'server' extra to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:685: Install Toil with the 'server' extra to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:676: Install Toil with the 'server' extra to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:721: Install Toil with the 'server' extra to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:619: Install Toil with the 'server' extra to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:600: Install Toil with the 'server' extra to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:668: Install Toil with the 'server' extra to include this test. 619s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:731: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 619s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:646: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 619s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:697: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 619s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:706: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 619s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:685: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 619s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:676: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 619s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:721: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 619s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:619: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 619s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:600: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 619s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:668: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 619s SKIPPED [7] ../../../../usr/lib/python3/dist-packages/_pytest/unittest.py:498: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:373: Set TOIL_AWS_KEYNAME to an AWS-stored SSH key to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:409: Set TOIL_AWS_KEYNAME to an AWS-stored SSH key to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:122: Set TOIL_AWS_KEYNAME to an AWS-stored SSH key to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:343: Set TOIL_AWS_KEYNAME to an AWS-stored SSH key to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:297: Set TOIL_AWS_KEYNAME to an AWS-stored SSH key to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:373: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:409: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:122: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:343: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:297: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:541: Install Toil with the 'server' extra to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:535: Install Toil with the 'server' extra to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:526: Install Toil with the 'server' extra to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py:533: Install Mesos (and Toil with the 'mesos' extra) to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:123: Install Mesos (and Toil with the 'mesos' extra) to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:147: Install Mesos (and Toil with the 'mesos' extra) to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py:255: Install Toil with the 'wdl' extra to include this test. 619s SKIPPED [3] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:96: Install Toil with the 'server' extra to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:245: Install Toil with the 'server' extra to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1568: Configure AWS credentials to include this test. 619s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:48: Install Toil with the 'server' extra to include this test. 619s FAILED lib/dockerTest.py::TestDocker::testDockerClean - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean0/working/test.txt' 619s FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_FORGO - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_FORGO0/working/test.txt' 619s FAILED docs/scriptsTest.py::ToilDocumentationTest::testDocker - RuntimeError: [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of f5d80754-bf08-4d77-8640-6a3bc2da12a5 in file:/tmp/tmp0vm7_i1ututorial_docker 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.lib.history] Workflow f5d80754-bf08-4d77-8640-6a3bc2da12a5 is a run of /usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s [2026-01-30T05:40:35+0000] [Thread-4 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:40:35: Job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v1 used 1.04x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:40:35+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmp0vm7_i1ututorial_docker kind-apiDockerCall/instance-9q8y1fwn. 619s [2026-01-30T05:40:35+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v1 619s Exit reason: None 619s [2026-01-30T05:40:35+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v2 619s [2026-01-30T05:40:35+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-9q8y1fwn" follows: 619s =========> 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v1 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v1) from description 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v1 619s [2026-01-30T05:40:35+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v1 used 1.04x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:40:35+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:40:35+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s [2026-01-30T05:40:35+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v2 with ID kind-apiDockerCall/instance-9q8y1fwn to 1 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 619s [2026-01-30T05:40:36+0000] [Thread-4 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:40:36: Job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:40:36+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmp0vm7_i1ututorial_docker kind-apiDockerCall/instance-9q8y1fwn. 619s [2026-01-30T05:40:36+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v3 619s Exit reason: None 619s [2026-01-30T05:40:36+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v5 619s [2026-01-30T05:40:36+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-9q8y1fwn" follows: 619s =========> 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4) from description 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4 619s [2026-01-30T05:40:35+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:40:35+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:40:35+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s [2026-01-30T05:40:36+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v5 with ID kind-apiDockerCall/instance-9q8y1fwn to 0 619s [2026-01-30T05:40:36+0000] [MainThread] [W] [toil.leader] Job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v6 is completely failed 619s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 619s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 619s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v6 619s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 619s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 619s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.lib.history] Workflow f5d80754-bf08-4d77-8640-6a3bc2da12a5 stopped. Success: False 619s [2026-01-30T05:40:40+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/tmp0vm7_i1ututorial_docker) 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py", line 20, in 619s toil.start(align) 619s ~~~~~~~~~~^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 619s return self._runMainLoop(rootJobDescription) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 619s ).run() 619s ~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 619s raise FailedJobsException( 619s ...<3 lines>... 619s ) 619s toil.exceptions.FailedJobsException: The job store '/tmp/tmp0vm7_i1ututorial_docker' contains 1 failed jobs: 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v6 619s Log from job "'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v6" follows: 619s =========> 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4 619s [2026-01-30T05:40:35+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4) from description 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4 619s [2026-01-30T05:40:35+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-9q8y1fwn v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:40:35+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:40:35+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_STOP - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_STOP0/working/test.txt' 619s FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_RM - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_RM0/working/test.txt' 619s FAILED lib/dockerTest.py::TestDocker::testDockerPipeChain - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v6 619s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v6" follows: 619s =========> 619s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4 619s [2026-01-30T05:40:53+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4 619s [2026-01-30T05:40:53+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-t4a93sh1 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:40:53+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 619s return apiDockerCall( 619s job, 619s ...<2 lines>... 619s privileged=True, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:40:53+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s FAILED lib/dockerTest.py::TestDocker::testDockerPipeChainErrorDetection - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChainErrorDetect0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v6 619s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v6" follows: 619s =========> 619s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4 619s [2026-01-30T05:40:59+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4 619s [2026-01-30T05:40:59+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-n3ndp5w9 v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:40:59+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 619s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 619s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:40:59+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChain - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v6 619s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v6" follows: 619s =========> 619s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4 619s [2026-01-30T05:41:05+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4 619s [2026-01-30T05:41:05+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-su26s9av v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:05+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 619s return apiDockerCall( 619s job, 619s ...<2 lines>... 619s privileged=True, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:05+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChainErrorDetection - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChainError0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v6 619s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v6" follows: 619s =========> 619s [2026-01-30T05:41:11+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:11+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:11+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4 619s [2026-01-30T05:41:11+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4 619s [2026-01-30T05:41:11+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-4iyb6omh v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:11+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 619s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 619s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:11+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s FAILED lib/dockerTest.py::TestDocker::testDockerLogs - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v6 619s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v6" follows: 619s =========> 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:19+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4 619s [2026-01-30T05:41:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4 619s [2026-01-30T05:41:20+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sivp4v4f v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:20+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:20+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Stream - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v6 619s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v6" follows: 619s =========> 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4 619s [2026-01-30T05:41:26+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4 619s [2026-01-30T05:41:26+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-th744hzf v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:26+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:26+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v6 619s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v6" follows: 619s =========> 619s [2026-01-30T05:41:32+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:32+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:32+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4 619s [2026-01-30T05:41:32+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4 619s [2026-01-30T05:41:32+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-aqx8erqz v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:32+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:32+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux_Stream - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v6 619s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v6" follows: 619s =========> 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4 619s [2026-01-30T05:41:37+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4 619s [2026-01-30T05:41:37+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-nrenh16w v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:41:37+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s PermissionError: [Errno 13] Permission denied 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 619s resp = conn.urlopen( 619s method=request.method, 619s ...<9 lines>... 619s chunked=chunked, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 619s retries = retries.increment( 619s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 619s raise reraise(type(error), error, _stacktrace) 619s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 619s raise value.with_traceback(tb) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 619s response = self._make_request( 619s conn, 619s ...<10 lines>... 619s **response_kw, 619s ) 619s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 619s conn.request( 619s ~~~~~~~~~~~~^ 619s method, 619s ^^^^^^^ 619s ...<6 lines>... 619s enforce_content_length=enforce_content_length, 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 619s self.endheaders() 619s ~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 619s self._send_output(message_body, encode_chunked=encode_chunked) 619s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 619s self.send(msg) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3.13/http/client.py", line 1057, in send 619s self.connect() 619s ~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 619s sock.connect(self.unix_socket) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 619s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s During handling of the above exception, another exception occurred: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 619s return self.version(api_version=False)["ApiVersion"] 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 619s return self._result(self._get(url), json=True) 619s ~~~~~~~~~^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 619s return f(self, *args, **kwargs) 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 619s return self.get(url, **self._set_request_timeout(kwargs)) 619s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 619s return self.request("GET", url, **kwargs) 619s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 619s resp = self.send(prep, **send_kwargs) 619s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 619s r = adapter.send(request, **kwargs) 619s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 619s raise ConnectionError(err, request=request) 619s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s The above exception was the direct cause of the following exception: 619s 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 619s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 619s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 619s out = apiDockerCall( 619s job, 619s ...<8 lines>... 619s demux=demux, 619s ) 619s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 619s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 619s return cls( 619s timeout=timeout, 619s ...<3 lines>... 619s **kwargs_from_env(**kwargs) 619s ) 619s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 619s self.api = APIClient(*args, **kwargs) 619s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 619s self._version = self._retrieve_server_version() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 619s raise DockerException( 619s f'Error while fetching server API version: {e}' 619s ) from e 619s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 619s 619s [2026-01-30T05:41:37+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s <========= 619s FAILED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithJobStoreFileObjects - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore' contains 2 failed jobs: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8, '_writer' kind-_writer/instance-yk1rpfbw v4 619s Log from job "'_follower' kind-EncapsulatedJob/instance-8yqn9nyw v8" follows: 619s =========> 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'c8b78540-44ef-4d4f-b67e-7bdbf1a1adac', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': True, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmplo15ag5f', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b/deferred/func3ipu26c2 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.worker] Parsed job description 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithJobStoreFileOb0/jobstore'. 619s [2026-01-30T05:43:21+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6) from description '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-ba43d1b9a6fc555696e17ecbeacf2c6b has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6) with ID (kind-EncapsulatedJob/instance-8yqn9nyw). 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6) with ID (kind-EncapsulatedJob/instance-8yqn9nyw) which wants 2147483648 of our 98062798848 bytes. 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98062798848 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98062798848 bytes 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:21+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-8yqn9nyw v6 used 10.15x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:21+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 619s self.evaluatePromisedRequirements() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 619s ].getValue() 619s ~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 619s return func(*self._args) 619s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 619s 619s [2026-01-30T05:43:21+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [pydot] pydot initializing 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [pydot] pydot 4.0.1 619s [2026-01-30T05:43:21+0000] [MainThread] [D] [pydot.core] pydot core module initializing 619s <========= 619s FAILED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithNonCachingFileStore - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore' contains 2 failed jobs: '_writer' kind-_writer/instance-lblqlima v4, '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8 619s Log from job "'_follower' kind-EncapsulatedJob/instance-0vvnaeqh v8" follows: 619s =========> 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '224f5500-e669-4936-8dfe-2cd58050a1dc', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/workdir', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'aws_batch_region': None, 'aws_batch_queue': None, 'aws_batch_job_role_arn': None, 'scale': 1, 'slurm_allocate_mem': True, 'slurm_default_all_mem': False, 'slurm_time': None, 'slurm_partition': None, 'slurm_gpu_partition': None, 'slurm_pe': None, 'slurm_args': '', 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'state_polling_timeout': 1200, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, 'symlink_job_store_reads': True, 'provisioner': None, 'nodeTypes': [], 'minNodes': [0], 'maxNodes': [10], 'targetTime': 1800, 'betaInertia': 0.1, 'scaleInterval': 60, 'metrics': False, 'assume_zero_overhead': False, 'preemptibleCompensation': 0.0, 'nodeStorage': 50, 'nodeStorageOverrides': [], 'maxServiceJobs': 9223372036854775807, 'maxPreemptibleServiceJobs': 9223372036854775807, 'deadlockWait': 60, 'deadlockCheckInterval': 30, 'defaultMemory': 2147483648, 'defaultCores': 2, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 4, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'stop_on_first_failure': False, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'job_store_timeout': 30, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/tmp64rjpwws', 'publish_workflow_metrics': None, 'environment': {}, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'statusWait': 3600, 'disableProgress': False, 'sseKey': None, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 0.01, 'logLevel': 'DEBUG', 'colored_logs': True, 'memory_is_product': False, 'workflowAttemptNumber': 0} 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428/deferred/funchi7kmzyz 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.worker] Parsed job description 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 619s [2026-01-30T05:43:29+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 619s [2026-01-30T05:43:29+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil] Using default docker appliance of quay.io/ucsc_cgl/toil:9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.13 as TOIL_APPLIANCE_SELF is not set. 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testPromisesWithNonCachingFile0/jobstore'. 619s [2026-01-30T05:43:30+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6) from description '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-1342b098ef205e0295f50d1d5c0c1428 has lockable filesystem type: tmpfs 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Running job 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 619s [2026-01-30T05:43:30+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-0vvnaeqh v6 used 7.38x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 619s [2026-01-30T05:43:30+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 619s Traceback (most recent call last): 619s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 619s job._runner( 619s ~~~~~~~~~~~^ 619s jobGraph=None, 619s ^^^^^^^^^^^^^^ 619s ...<2 lines>... 619s defer=defer, 619s ^^^^^^^^^^^^ 619s ) 619s ^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 619s returnValues = self._run(jobGraph=None, fileStore=fileStore) 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 619s return self.run(fileStore) 619s ~~~~~~~~^^^^^^^^^^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 619s self.evaluatePromisedRequirements() 619s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 619s ].getValue() 619s ~~~~~~~~^^ 619s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 619s return func(*self._args) 619s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 619s 619s [2026-01-30T05:43:30+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [pydot] pydot initializing 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [pydot] pydot 4.0.1 619s [2026-01-30T05:43:30+0000] [MainThread] [D] [pydot.core] pydot core module initializing 619s <========= 619s ERROR src/importExportFileTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py'. 619s Hint: make sure your test modules/packages have valid Python names. 619s Traceback: 619s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 619s mod = import_path( 619s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 619s importlib.import_module(module_name) 619s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 619s return _bootstrap._gcd_import(name[level:], package, level) 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s :1398: in _gcd_import 619s ??? 619s :1371: in _find_and_load 619s ??? 619s :1342: in _find_and_load_unlocked 619s ??? 619s :938: in _load_unlocked 619s ??? 619s :759: in exec_module 619s ??? 619s :491: in _call_with_frames_removed 619s ??? 619s /usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py:30: in 619s from pytest_subtests import SubTests 619s E ModuleNotFoundError: No module named 'pytest_subtests' 619s ERROR src/jobEncapsulationTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py'. 619s Hint: make sure your test modules/packages have valid Python names. 619s Traceback: 619s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 619s mod = import_path( 619s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 619s importlib.import_module(module_name) 619s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 619s return _bootstrap._gcd_import(name[level:], package, level) 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s :1398: in _gcd_import 619s ??? 619s :1371: in _find_and_load 619s ??? 619s :1342: in _find_and_load_unlocked 619s ??? 619s :938: in _load_unlocked 619s ??? 619s :759: in exec_module 619s ??? 619s :491: in _call_with_frames_removed 619s ??? 619s /usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py:17: in 619s from toil.test.src.jobTest import fn1Test 619s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 619s from pytest_subtests import SubTests 619s E ModuleNotFoundError: No module named 'pytest_subtests' 619s ERROR src/jobTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobTest.py'. 619s Hint: make sure your test modules/packages have valid Python names. 619s Traceback: 619s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 619s mod = import_path( 619s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 619s importlib.import_module(module_name) 619s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 619s return _bootstrap._gcd_import(name[level:], package, level) 619s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 619s :1398: in _gcd_import 619s ??? 619s :1371: in _find_and_load 619s ??? 619s :1342: in _find_and_load_unlocked 619s ??? 619s :938: in _load_unlocked 619s ??? 619s :759: in exec_module 619s ??? 619s :491: in _call_with_frames_removed 619s ??? 619s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 619s from pytest_subtests import SubTests 619s E ModuleNotFoundError: No module named 'pytest_subtests' 619s = 15 failed, 224 passed, 136 skipped, 3 errors, 24 subtests passed in 466.96s (0:07:46) = 619s E: pybuild pybuild:483: test: plugin pyproject failed with: exit code=1: cd /tmp/autopkgtest.leevCg/autopkgtest_tmp/build; python3.14 -m pytest -n 4 --dist loadscope -vv -W ignore -k "not (testVirtualEnv or DockstoreLookupTest or testMultiplejobs or testServices)" -m "not slow" --ignore /usr/lib/python3/dist-packages/toil/test/lib/aws/test_s3.py --ignore /usr/lib/python3/dist-packages/toil/test/provisioners/aws/awsProvisionerTest.py --ignore /usr/lib/python3/dist-packages/toil/test/wdl/wdltoil_test.py --ignore /usr/lib/python3/dist-packages/toil/test/cwl/cwlTest.py --ignore /usr/lib/python3/dist-packages/toil/test/lib/test_ec2.py --ignore /usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py --ignore /usr/lib/python3/dist-packages/toil/test/lib/aws/test_iam.py --ignore /usr/lib/python3/dist-packages/toil/test/provisioners/clusterTest.py --ignore /usr/lib/python3/dist-packages/toil/test/wdl/wdltoil_test_kubernetes.py --ignore /usr/lib/python3/dist-packages/toil/test/cactus/test_cactus_integration.py --pyargs toil.test 619s I: pybuild base:384: cd /tmp/autopkgtest.leevCg/autopkgtest_tmp/build; python3.13 -m pytest -n 4 --dist loadscope -vv -W ignore -k "not (testVirtualEnv or DockstoreLookupTest or testMultiplejobs or testServices)" -m "not slow" --ignore /usr/lib/python3/dist-packages/toil/test/lib/aws/test_s3.py --ignore /usr/lib/python3/dist-packages/toil/test/provisioners/aws/awsProvisionerTest.py --ignore /usr/lib/python3/dist-packages/toil/test/wdl/wdltoil_test.py --ignore /usr/lib/python3/dist-packages/toil/test/cwl/cwlTest.py --ignore /usr/lib/python3/dist-packages/toil/test/lib/test_ec2.py --ignore /usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py --ignore /usr/lib/python3/dist-packages/toil/test/lib/aws/test_iam.py --ignore /usr/lib/python3/dist-packages/toil/test/provisioners/clusterTest.py --ignore /usr/lib/python3/dist-packages/toil/test/wdl/wdltoil_test_kubernetes.py --ignore /usr/lib/python3/dist-packages/toil/test/cactus/test_cactus_integration.py --pyargs toil.test 621s ============================= test session starts ============================== 621s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.13 621s cachedir: .pytest_cache 621s rootdir: /tmp/autopkgtest.leevCg/autopkgtest_tmp/build 621s configfile: setup.cfg 621s plugins: timeout-2.4.0, typeguard-4.4.4, cwltest-2.6.20251216093331, xdist-3.8.0, pytest_httpserver-1.1.3 621s created: 4/4 workers 621s 4 workers [375 items] 621s 621s scheduling tests via LoadScopeScheduling 621s 621s batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_default_gpu_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 621s jobStores/jobStoreTest.py::GoogleJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw2] [ 0%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::AWSJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::FileJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw0] [ 0%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::GoogleJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::AWSJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw2] [ 0%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw0] [ 1%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::GoogleJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::AWSJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw0] [ 1%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::AWSJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw2] [ 1%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw2] [ 1%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::GoogleJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw2] [ 2%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::GoogleJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw2] [ 2%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw0] [ 2%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::AWSJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw0] [ 2%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw2] [ 3%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::AWSJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw0] [ 3%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::AWSJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw2] [ 3%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::GoogleJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw0] [ 4%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::AWSJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw2] [ 4%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw0] [ 4%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::AWSJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw2] [ 4%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw0] [ 5%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::AWSJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw2] [ 5%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw0] [ 5%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw2] [ 5%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::AWSJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s jobStores/jobStoreTest.py::GoogleJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 621s [gw0] [ 6%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw2] [ 6%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw0] [ 6%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::testMultiThreadImportFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw0] [ 6%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testMultiThreadImportFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::testOverlargeJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw0] [ 7%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testOverlargeJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw2] [ 7%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw2] [ 7%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw0] [ 8%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw2] [ 8%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw0] [ 8%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw0] [ 8%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw2] [ 9%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw0] [ 9%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw0] [ 9%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw2] [ 9%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw0] [ 10%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw2] [ 10%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw0] [ 10%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw0] [ 10%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw2] [ 11%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw0] [ 11%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw3] [ 11%] PASSED batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_default_gpu_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw2] [ 12%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw2] [ 12%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw0] [ 12%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw0] [ 12%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_get_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw2] [ 13%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw0] [ 13%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw0] [ 13%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw0] [ 13%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw0] [ 14%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw2] [ 14%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw3] [ 14%] PASSED batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_get_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw2] [ 14%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw0] [ 15%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw0] [ 15%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s batchSystems/test_slurm.py::SlurmTest::test_any_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw0] [ 15%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw2] [ 16%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw0] [ 16%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw0] [ 16%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw0] [ 16%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw2] [ 17%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw2] [ 17%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw3] [ 17%] PASSED batchSystems/test_slurm.py::SlurmTest::test_any_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw0] [ 17%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw0] [ 18%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw2] [ 18%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s docs/scriptsTest.py::ToilDocumentationTest::testArguments <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw2] [ 18%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw1] [ 18%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::FileJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw2] [ 19%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw3] [ 19%] PASSED batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw2] [ 19%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_mix_sacct_scontrol <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw2] [ 20%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw2] [ 20%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s [gw2] [ 20%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 622s lib/dockerTest.py::TestDocker::testDockerClean <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 622s [gw1] [ 20%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::FileJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw3] [ 21%] PASSED batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_mix_sacct_scontrol <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw1] [ 21%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw3] [ 21%] PASSED batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw1] [ 21%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::FileJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw1] [ 22%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw1] [ 22%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s jobStores/jobStoreTest.py::FileJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 622s [gw3] [ 22%] PASSED batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_sacct_raises_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 22%] PASSED batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_sacct_raises_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_sacct_raises_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 23%] PASSED batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_sacct_raises_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_some_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 23%] PASSED batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_some_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_argument_list_too_big <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 23%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_argument_list_too_big <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 27%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 27%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 27%] PASSED batchSystems/test_slurm.py::SlurmTest::test_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_export <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 28%] PASSED batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_export <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 28%] PASSED batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_time <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s [gw3] [ 28%] PASSED batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_time <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 622s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 622s [gw1] [ 28%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 623s jobStores/jobStoreTest.py::FileJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 623s [gw1] [ 29%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 625s jobStores/jobStoreTest.py::FileJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 625s [gw3] [ 29%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 625s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 625s [gw0] [ 29%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testArguments <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 626s docs/scriptsTest.py::ToilDocumentationTest::testDocker <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 626s [gw2] [ 29%] FAILED lib/dockerTest.py::TestDocker::testDockerClean <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 627s lib/dockerTest.py::TestDocker::testDockerClean_CRx_FORGO <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 630s [gw3] [ 30%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=True] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 631s [gw3] [ 30%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 631s [gw2] [ 30%] FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_FORGO <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 632s lib/dockerTest.py::TestDocker::testDockerClean_CRx_STOP <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 632s [gw0] [ 30%] FAILED docs/scriptsTest.py::ToilDocumentationTest::testDocker <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 632s docs/scriptsTest.py::ToilDocumentationTest::testDynamic <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 635s [gw3] [ 30%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 635s [gw3] [ 30%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 635s [gw2] [ 30%] FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_STOP <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 638s lib/dockerTest.py::TestDocker::testDockerClean_CRx_RM <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 641s [gw3] [ 30%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=True] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 641s [gw2] [ 31%] FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_RM <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 642s lib/dockerTest.py::TestDocker::testDockerPipeChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 646s [gw3] [ 31%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 648s [gw3] [ 31%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 648s [gw2] [ 31%] FAILED lib/dockerTest.py::TestDocker::testDockerPipeChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 650s lib/dockerTest.py::TestDocker::testDockerPipeChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 650s [gw3] [ 31%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 650s [gw3] [ 31%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 652s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 652s [gw1] [ 31%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 652s jobStores/jobStoreTest.py::FileJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 652s [gw1] [ 32%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 652s jobStores/jobStoreTest.py::FileJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 652s [gw3] [ 32%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 653s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 653s [gw2] [ 32%] FAILED lib/dockerTest.py::TestDocker::testDockerPipeChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 655s lib/dockerTest.py::TestDocker::testNonCachingDockerChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 655s [gw3] [ 32%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 656s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 656s [gw0] [ 33%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testDynamic <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 657s docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 657s [gw3] [ 33%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 659s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 659s [gw2] [ 33%] FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 659s lib/dockerTest.py::TestDocker::testNonCachingDockerChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 659s [gw0] [ 33%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 661s docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 661s [gw3] [ 34%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 664s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 664s [gw2] [ 34%] FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 667s lib/dockerTest.py::TestDocker::testDockerLogs <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 667s [gw0] [ 34%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 670s docs/scriptsTest.py::ToilDocumentationTest::testHelloworld <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 670s [gw0] [ 34%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testHelloworld <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 673s docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 673s [gw2] [ 35%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 673s lib/dockerTest.py::TestDocker::testDockerLogs_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 673s [gw0] [ 35%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 676s docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 676s [gw0] [ 35%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 678s docs/scriptsTest.py::ToilDocumentationTest::testJobFunctions <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 678s [gw2] [ 36%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 679s lib/dockerTest.py::TestDocker::testDockerLogs_Demux <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 679s [gw0] [ 36%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testJobFunctions <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 682s docs/scriptsTest.py::ToilDocumentationTest::testManaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 682s [gw0] [ 36%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testManaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 683s docs/scriptsTest.py::ToilDocumentationTest::testManaging2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 683s [gw2] [ 36%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 685s lib/dockerTest.py::TestDocker::testDockerLogs_Demux_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 685s [gw0] [ 37%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testManaging2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 688s docs/scriptsTest.py::ToilDocumentationTest::testPromises <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 688s [gw2] [ 37%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 688s src/dockerCheckTest.py::DockerCheckTest::testApplianceParser <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 688s [gw2] [ 37%] PASSED src/dockerCheckTest.py::DockerCheckTest::testApplianceParser <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 689s src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 689s [gw0] [ 37%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testPromises <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 689s docs/scriptsTest.py::ToilDocumentationTest::testPromises2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 689s [gw2] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 689s src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 689s [gw2] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 689s src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 689s [gw2] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 690s src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 690s [gw2] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 690s src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 690s [gw2] [ 39%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 690s src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 690s [gw2] [ 39%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 690s src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 690s [gw2] [ 39%] PASSED src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 690s src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 690s [gw2] [ 40%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 690s src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 690s [gw2] [ 40%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 690s src/dockerCheckTest.py::DockerCheckTest::testToilQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 690s [gw2] [ 40%] PASSED src/dockerCheckTest.py::DockerCheckTest::testToilQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 690s provisioners/clusterScalerTest.py::ClusterScalerTest::testBetaInertia <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 690s [gw2] [ 40%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testBetaInertia <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 690s provisioners/clusterScalerTest.py::ClusterScalerTest::testMaxNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 690s [gw2] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testMaxNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 690s provisioners/clusterScalerTest.py::ClusterScalerTest::testMinNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 690s [gw2] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testMinNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 690s provisioners/clusterScalerTest.py::ClusterScalerTest::testNoLaunchingIfDeltaAlreadyMet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 690s [gw2] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testNoLaunchingIfDeltaAlreadyMet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 690s provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitIsSet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 690s [gw2] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitIsSet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 690s provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitResponse <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s [gw2] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitResponse <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s provisioners/clusterScalerTest.py::ClusterScalerTest::testRounding <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s [gw2] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testRounding <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_large <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s [gw2] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_large <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_observed <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s [gw2] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_observed <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_small <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s [gw2] [ 43%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_small <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s server/serverTest.py::ToilWESServerWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 43%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 43%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 47%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 47%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 47%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s [gw2] [ 51%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 691s provisioners/clusterScalerTest.py::BinPackingTest::testAddingInitialNode <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s [gw2] [ 51%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testAddingInitialNode <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s provisioners/clusterScalerTest.py::BinPackingTest::testHighTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s [gw2] [ 51%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testHighTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s provisioners/clusterScalerTest.py::BinPackingTest::testJobTooLargeForAllNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s [gw2] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testJobTooLargeForAllNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s provisioners/clusterScalerTest.py::BinPackingTest::testLongRunningJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s [gw2] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testLongRunningJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s provisioners/clusterScalerTest.py::BinPackingTest::testLowTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s [gw2] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testLowTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s provisioners/clusterScalerTest.py::BinPackingTest::testPackingOneShape <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s [gw2] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testPackingOneShape <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s provisioners/clusterScalerTest.py::BinPackingTest::testPathologicalCase <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s [gw2] [ 53%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testPathologicalCase <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s provisioners/clusterScalerTest.py::BinPackingTest::testSorting <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s [gw2] [ 53%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testSorting <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s provisioners/clusterScalerTest.py::BinPackingTest::testZeroResourceJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 691s [gw2] [ 53%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testZeroResourceJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 692s utils/utilsTest.py::TestUtils::test_config_functionality <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 692s [gw2] [ 53%] PASSED utils/utilsTest.py::TestUtils::test_config_functionality <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 710s utils/utilsTest.py::TestUtils::testUtilsSort <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 710s [gw1] [ 54%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s [gw1] [ 54%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s [gw1] [ 54%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s [gw1] [ 54%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s [gw1] [ 55%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s [gw1] [ 55%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s [gw1] [ 55%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s [gw1] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s [gw1] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s [gw1] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s [gw1] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s [gw1] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s [gw1] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::test_file_link_imports <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s [gw1] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_file_link_imports <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_does_not_leak_symlinks <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s [gw1] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_does_not_leak_symlinks <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_init_preserves_symlink_path <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s [gw1] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_init_preserves_symlink_path <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::test_symlink_read_control <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s [gw1] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_symlink_read_control <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 710s [gw1] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 710s [gw1] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 710s [gw1] [ 59%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 710s [gw1] [ 59%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 710s [gw1] [ 59%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 710s [gw1] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 710s [gw1] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 710s [gw1] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 710s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 710s [gw1] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 711s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 711s [gw1] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 711s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 711s [gw1] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 711s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 711s [gw1] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 711s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 711s [gw1] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 711s src/miscTests.py::TestMisc::testIDStability <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 711s [gw1] [ 62%] PASSED src/miscTests.py::TestMisc::testIDStability <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 711s src/miscTests.py::TestMisc::test_atomic_install <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 711s [gw1] [ 62%] PASSED src/miscTests.py::TestMisc::test_atomic_install <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 711s src/miscTests.py::TestMisc::test_atomic_install_dev <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 711s [gw1] [ 62%] PASSED src/miscTests.py::TestMisc::test_atomic_install_dev <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 711s src/miscTests.py::TestMisc::test_atomic_context_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 711s [gw1] [ 62%] PASSED src/miscTests.py::TestMisc::test_atomic_context_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 711s src/miscTests.py::TestMisc::test_atomic_context_error <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 711s [gw1] [ 63%] PASSED src/miscTests.py::TestMisc::test_atomic_context_error <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 711s src/miscTests.py::TestMisc::test_call_command_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 711s [gw1] [ 63%] PASSED src/miscTests.py::TestMisc::test_call_command_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 711s src/miscTests.py::TestMisc::test_call_command_err <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 711s [gw1] [ 63%] PASSED src/miscTests.py::TestMisc::test_call_command_err <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 711s lib/test_url.py::TestURLAccess::test_get_url_access <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 711s [gw1] [ 64%] PASSED lib/test_url.py::TestURLAccess::test_get_url_access <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 711s lib/test_url.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 711s [gw1] [ 64%] SKIPPED lib/test_url.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 711s lib/test_url.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 711s [gw1] [ 64%] SKIPPED lib/test_url.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 711s lib/test_url.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 711s [gw1] [ 64%] SKIPPED lib/test_url.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 711s lib/test_url.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 711s [gw1] [ 65%] SKIPPED lib/test_url.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 711s lib/test_url.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 711s [gw1] [ 65%] SKIPPED lib/test_url.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 711s lib/url_plugin_test.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 711s [gw1] [ 65%] PASSED lib/url_plugin_test.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 711s lib/url_plugin_test.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 711s [gw1] [ 65%] PASSED lib/url_plugin_test.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 711s lib/url_plugin_test.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 711s [gw1] [ 66%] PASSED lib/url_plugin_test.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 711s lib/url_plugin_test.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 711s [gw1] [ 66%] PASSED lib/url_plugin_test.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 711s lib/url_plugin_test.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 711s [gw1] [ 66%] PASSED lib/url_plugin_test.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 711s lib/url_plugin_test.py::TestURLAccess::test_url_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 711s [gw1] [ 66%] PASSED lib/url_plugin_test.py::TestURLAccess::test_url_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 713s src/retainTempDirTest.py::TestCleanWorkDir::testNever <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 713s [gw1] [ 67%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testNever <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 716s src/retainTempDirTest.py::TestCleanWorkDir::testAlways <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 716s [gw1] [ 67%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testAlways <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 717s src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 717s [gw0] [ 67%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testPromises2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 720s docs/scriptsTest.py::ToilDocumentationTest::testQuickstart <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 720s [gw0] [ 68%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testQuickstart <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 721s docs/scriptsTest.py::ToilDocumentationTest::testRequirements <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 721s [gw1] [ 68%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 725s src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithNoError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 725s [gw1] [ 68%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithNoError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 729s src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 729s [gw0] [ 68%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testRequirements <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 731s docs/scriptsTest.py::ToilDocumentationTest::testStaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 731s [gw1] [ 69%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 732s src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithSuccess <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 732s [gw0] [ 69%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testStaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 733s docs/scriptsTest.py::ToilDocumentationTest::testStats <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 733s [gw1] [ 69%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithSuccess <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 733s lib/aws/test_utils.py::TagGenerationTest::test_build_tag <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 733s [gw1] [ 69%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_build_tag <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 733s lib/aws/test_utils.py::TagGenerationTest::test_build_tag_with_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 733s [gw1] [ 70%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_build_tag_with_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 733s lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 733s [gw1] [ 70%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 733s lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 733s [gw1] [ 70%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 733s lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 733s [gw1] [ 70%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 733s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s [gw1] [ 71%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s [gw1] [ 71%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s [gw1] [ 71%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s [gw1] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s [gw1] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s [gw1] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s [gw1] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s [gw1] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s [gw1] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s [gw1] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 733s src/resourceTest.py::TestResource::testStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 733s [gw1] [ 73%] PASSED src/resourceTest.py::TestResource::testStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 733s src/resourceTest.py::TestResource::testPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 733s [gw1] [ 74%] PASSED src/resourceTest.py::TestResource::testPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 733s src/resourceTest.py::TestResource::testStandAloneInPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 733s [gw1] [ 74%] PASSED src/resourceTest.py::TestResource::testStandAloneInPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 733s src/resourceTest.py::TestResource::testBuiltIn <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 733s [gw1] [ 74%] PASSED src/resourceTest.py::TestResource::testBuiltIn <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 734s src/resourceTest.py::TestResource::testNonPyStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 734s [gw1] [ 74%] PASSED src/resourceTest.py::TestResource::testNonPyStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 738s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 738s [gw1] [ 75%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 741s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithClassMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 741s [gw1] [ 75%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithClassMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 745s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithLambda <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 745s [gw1] [ 75%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithLambda <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 749s src/deferredFunctionTest.py::TestDeferredFunction::testBatchSystemCleanupCanHandleWorkerDeaths <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 749s [gw1] [ 76%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testBatchSystemCleanupCanHandleWorkerDeaths <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 749s src/miscTests.py::TestPanic::test_panic_by_hand <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 749s [gw1] [ 76%] PASSED src/miscTests.py::TestPanic::test_panic_by_hand <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 749s src/miscTests.py::TestPanic::test_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 749s [gw1] [ 76%] PASSED src/miscTests.py::TestPanic::test_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 749s src/miscTests.py::TestPanic::test_panic_with_secondary <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 749s [gw1] [ 76%] PASSED src/miscTests.py::TestPanic::test_panic_with_secondary <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 749s src/miscTests.py::TestPanic::test_nested_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 749s [gw1] [ 77%] PASSED src/miscTests.py::TestPanic::test_nested_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 749s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 749s [gw1] [ 77%] PASSED batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 750s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 750s [gw1] [ 77%] PASSED batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 750s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_still_running <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 750s [gw1] [ 77%] PASSED batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_still_running <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 750s lib/test_conversions.py::ConversionTest::test_convert <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 750s [gw1] [ 78%] PASSED lib/test_conversions.py::ConversionTest::test_convert <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 750s lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 750s [gw1] [ 78%] PASSED lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 750s lib/test_conversions.py::ConversionTest::test_human2bytes <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 750s [gw1] [ 78%] PASSED lib/test_conversions.py::ConversionTest::test_human2bytes <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 750s lib/test_history.py::TestHistory::test_history_submittable_detection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 750s [gw1] [ 78%] PASSED lib/test_history.py::TestHistory::test_history_submittable_detection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 750s lib/test_history.py::TestHistory::test_history_deletion <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 750s [gw1] [ 79%] PASSED lib/test_history.py::TestHistory::test_history_deletion <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 750s lib/test_history.py::TestHistory::test_history_size_limit <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 750s [gw1] [ 79%] PASSED lib/test_history.py::TestHistory::test_history_size_limit <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 750s server/serverTest.py::ToilWESServerBenchTest::test_get_service_info <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 750s [gw1] [ 79%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_get_service_info <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 750s server/serverTest.py::ToilWESServerBenchTest::test_health <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 750s [gw1] [ 80%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_health <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 750s server/serverTest.py::ToilWESServerBenchTest::test_home <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 750s [gw1] [ 80%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_home <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 750s src/busTest.py::TestMessageBus::test_enum_ints_in_file <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 750s [gw1] [ 80%] PASSED src/busTest.py::TestMessageBus::test_enum_ints_in_file <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 750s src/busTest.py::TestMessageBus::test_cross_thread_messaging <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 750s [gw1] [ 80%] PASSED src/busTest.py::TestMessageBus::test_cross_thread_messaging <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 758s src/busTest.py::TestMessageBus::test_restart_without_bus_path <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 758s [gw0] [ 81%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testStats <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 760s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 760s [gw1] [ 81%] PASSED src/busTest.py::TestMessageBus::test_restart_without_bus_path <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 761s src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 762s [gw0] [ 81%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 762s [gw1] [ 81%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 763s src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 767s [gw0] [ 81%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 770s [gw0] [ 81%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 772s [gw0] [ 81%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 772s [gw0] [ 81%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 772s [gw1] [ 82%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 775s src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 775s [gw0] [ 82%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 775s [gw1] [ 82%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 777s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 780s [gw0] [ 82%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 780s [gw0] [ 82%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 780s [gw0] [ 82%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 782s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 782s [gw0] [ 82%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 784s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 784s [gw1] [ 82%] PASSED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 791s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 791s [gw0] [ 83%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 793s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 793s [gw1] [ 83%] PASSED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 796s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 796s [gw0] [ 83%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 799s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 799s [gw0] [ 84%] SUBPASSED[Testing readwrite file permissions 799s [executable: True] 799s [caching: True] 802s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 802s [gw1] [ 84%] PASSED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 802s src/promisedRequirementTest.py::TestMesosPromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 802s [gw1] [ 84%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 802s src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 802s [gw1] [ 84%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 802s src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 802s [gw1] [ 85%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 802s utils/toilDebugTest.py::TestDebugJob::test_run_job <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 802s [gw0] [ 85%] SUBPASSED[Testing readwrite file permissions 802s [executable: True] 802s [caching: False] 806s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 806s [gw0] [ 85%] SUBPASSED[Testing readwrite file permissions 806s [executable: False] 806s [caching: True] 808s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 808s [gw2] [ 85%] PASSED utils/utilsTest.py::TestUtils::testUtilsSort <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 809s utils/utilsTest.py::TestUtils::testUnicodeSupport <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 809s [gw0] [ 85%] SUBPASSED[Testing readwrite file permissions 809s [executable: False] 809s [caching: False] 809s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 809s [gw0] [ 85%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 809s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 809s [gw0] [ 85%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 810s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 810s [gw1] [ 85%] PASSED utils/toilDebugTest.py::TestDebugJob::test_run_job <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 810s utils/toilDebugTest.py::TestDebugJob::test_print_job_info <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 810s [gw2] [ 86%] PASSED utils/utilsTest.py::TestUtils::testUnicodeSupport <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 815s utils/utilsTest.py::TestUtils::testGetPIDStatus <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 815s [gw0] [ 86%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 815s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 815s [gw0] [ 86%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 815s __init__.py::toil.test.make_tests <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 815s [gw0] [ 86%] PASSED __init__.py::toil.test.make_tests <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 817s __init__.py::toil.test.timeLimit <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 817s [gw2] [ 87%] PASSED utils/utilsTest.py::TestUtils::testGetPIDStatus <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 817s utils/utilsTest.py::TestUtils::testGetStatusFailedToilWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 817s [gw1] [ 87%] PASSED utils/toilDebugTest.py::TestDebugJob::test_print_job_info <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 817s utils/toilDebugTest.py::TestDebugJob::test_retrieve_task_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 817s [gw1] [ 87%] SKIPPED utils/toilDebugTest.py::TestDebugJob::test_retrieve_task_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 817s options/options.py::OptionsTest::test_caching_option_priority <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 817s [gw1] [ 88%] PASSED options/options.py::OptionsTest::test_caching_option_priority <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 817s options/options.py::OptionsTest::test_default_caching_slurm <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 817s [gw1] [ 88%] PASSED options/options.py::OptionsTest::test_default_caching_slurm <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 817s src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 817s [gw1] [ 88%] PASSED src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 817s src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 817s [gw1] [ 88%] PASSED src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 817s src/threadingTest.py::TestThreading::testGlobalMutexOrdering <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 817s [gw0] [ 89%] PASSED __init__.py::toil.test.timeLimit <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 817s server/serverTest.py::AWSStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 817s [gw0] [ 89%] SKIPPED server/serverTest.py::AWSStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 817s server/serverTest.py::AWSStateStoreTest::test_state_store_paths <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 817s [gw0] [ 89%] SKIPPED server/serverTest.py::AWSStateStoreTest::test_state_store_paths <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 817s batchSystems/test_lsf_helper.py::LSFHelperTest::test_parse_mem_and_cmd_from_output <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_lsf_helper.py 817s [gw0] [ 89%] PASSED batchSystems/test_lsf_helper.py::LSFHelperTest::test_parse_mem_and_cmd_from_output <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_lsf_helper.py 817s jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 817s [gw0] [ 90%] SKIPPED jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 817s lib/test_misc.py::UserNameAvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 817s [gw0] [ 90%] PASSED lib/test_misc.py::UserNameAvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 817s lib/test_misc.py::UserNameUnvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 817s [gw0] [ 90%] PASSED lib/test_misc.py::UserNameUnvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 817s lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 817s [gw0] [ 90%] PASSED lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 817s mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue <- ../../../../usr/lib/python3/dist-packages/toil/test/mesos/MesosDataStructuresTest.py 817s [gw0] [ 91%] PASSED mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue <- ../../../../usr/lib/python3/dist-packages/toil/test/mesos/MesosDataStructuresTest.py 817s provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/provisionerTest.py 817s [gw0] [ 91%] PASSED provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/provisionerTest.py 817s server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 817s [gw0] [ 91%] SKIPPED server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 817s server/serverTest.py::FileStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 817s [gw0] [ 92%] SKIPPED server/serverTest.py::FileStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 817s server/serverTest.py::FileStateStoreURLTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 817s [gw0] [ 92%] SKIPPED server/serverTest.py::FileStateStoreURLTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 822s src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried <- ../../../../usr/lib/python3/dist-packages/toil/test/src/checkpointTest.py 822s [gw2] [ 92%] PASSED utils/utilsTest.py::TestUtils::testGetStatusFailedToilWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 824s utils/utilsTest.py::TestUtils::testGetStatusFailedCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 824s [gw1] [ 92%] PASSED src/threadingTest.py::TestThreading::testGlobalMutexOrdering <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 826s src/threadingTest.py::TestThreading::testLastProcessStanding <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 826s [gw0] [ 93%] PASSED src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried <- ../../../../usr/lib/python3/dist-packages/toil/test/src/checkpointTest.py 828s src/environmentTest.py::EnvironmentTest::test_environment <- ../../../../usr/lib/python3/dist-packages/toil/test/src/environmentTest.py 828s [gw1] [ 93%] PASSED src/threadingTest.py::TestThreading::testLastProcessStanding <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 828s batchSystems/batch_system_plugin_test.py::BatchSystemPluginTest::test_batchsystem_plugin_installable <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batch_system_plugin_test.py 828s [gw1] [ 93%] PASSED batchSystems/batch_system_plugin_test.py::BatchSystemPluginTest::test_batchsystem_plugin_installable <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batch_system_plugin_test.py 828s src/jobServiceTest.py::TestJobService::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 828s [gw2] [ 93%] PASSED utils/utilsTest.py::TestUtils::testGetStatusFailedCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 834s utils/utilsTest.py::TestUtils::testGetStatusSuccessfulCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 834s [gw2] [ 94%] PASSED utils/utilsTest.py::TestUtils::testGetStatusSuccessfulCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 841s utils/utilsTest.py::TestUtils::testPrintJobLog <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 841s [gw2] [ 94%] PASSED utils/utilsTest.py::TestUtils::testPrintJobLog <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 843s utils/utilsTest.py::TestUtils::testRestartAttribute <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 843s [gw0] [ 94%] PASSED src/environmentTest.py::EnvironmentTest::test_environment <- ../../../../usr/lib/python3/dist-packages/toil/test/src/environmentTest.py 850s src/helloWorldTest.py::HelloWorldTest::testHelloWorld <- ../../../../usr/lib/python3/dist-packages/toil/test/src/helloWorldTest.py 850s [gw0] [ 94%] PASSED src/helloWorldTest.py::HelloWorldTest::testHelloWorld <- ../../../../usr/lib/python3/dist-packages/toil/test/src/helloWorldTest.py 854s src/jobServiceTest.py::TestPerfectServicet::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 854s [gw1] [ 95%] PASSED src/jobServiceTest.py::TestJobService::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 860s src/promisesTest.py::CachedUnpicklingJobStoreTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 860s [gw1] [ 95%] PASSED src/promisesTest.py::CachedUnpicklingJobStoreTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 863s src/promisesTest.py::ChainedIndexedPromisesTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 863s [gw1] [ 95%] PASSED src/promisesTest.py::ChainedIndexedPromisesTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 863s src/workerTest.py::WorkerTests::testNextChainable <- ../../../../usr/lib/python3/dist-packages/toil/test/src/workerTest.py 863s [gw1] [ 96%] PASSED src/workerTest.py::WorkerTests::testNextChainable <- ../../../../usr/lib/python3/dist-packages/toil/test/src/workerTest.py 865s utils/toilDebugTest.py::testFetchJobStoreFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 865s [gw2] [ 96%] PASSED utils/utilsTest.py::TestUtils::testRestartAttribute <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 868s src/promisesTest.py::PathIndexingPromiseTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 868s [gw2] [ 96%] PASSED src/promisesTest.py::PathIndexingPromiseTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 871s src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger <- ../../../../usr/lib/python3/dist-packages/toil/test/src/realtimeLoggerTest.py 871s [gw2] [ 96%] PASSED src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger <- ../../../../usr/lib/python3/dist-packages/toil/test/src/realtimeLoggerTest.py 871s [gw1] [ 97%] PASSED utils/toilDebugTest.py::testFetchJobStoreFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 871s utils/toilKillTest.py::TestToilKill::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 871s [gw1] [ 97%] SKIPPED utils/toilKillTest.py::TestToilKill::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 871s utils/toilKillTest.py::TestToilKillWithAWSJobStore::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 876s [gw1] [ 97%] SKIPPED utils/toilKillTest.py::TestToilKillWithAWSJobStore::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 876s [gw0] [ 97%] PASSED src/jobServiceTest.py::TestPerfectServicet::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 884s src/resumabilityTest.py::TestResumability::test_chaining <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resumabilityTest.py 884s [gw0] [ 98%] PASSED src/resumabilityTest.py::TestResumability::test_chaining <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resumabilityTest.py 887s src/systemTest.py::TestSystem::testAtomicityOfNonEmptyDirectoryRenames <- ../../../../usr/lib/python3/dist-packages/toil/test/src/systemTest.py 914s [gw0] [ 98%] PASSED src/systemTest.py::TestSystem::testAtomicityOfNonEmptyDirectoryRenames <- ../../../../usr/lib/python3/dist-packages/toil/test/src/systemTest.py 914s [gw3] [ 98%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 922s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 922s [gw3] [ 98%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 929s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 929s [gw3] [ 99%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 931s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 931s [gw3] [ 99%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 934s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 934s [gw3] [ 99%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 936s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 936s [gw3] [100%] SUBPASSED[Testing readwrite file permissions 936s [executable: True] 936s [caching: True] 939s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 939s [gw3] [100%] SUBPASSED[Testing readwrite file permissions 939s [executable: True] 939s [caching: False] 941s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 941s [gw3] [100%] SUBPASSED[Testing readwrite file permissions 941s [executable: False] 941s [caching: True] 944s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 944s [gw3] [100%] SUBPASSED[Testing readwrite file permissions 944s [executable: False] 944s [caching: False] 944s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 945s [gw3] [100%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 945s 945s ==================================== ERRORS ==================================== 945s _________________ ERROR collecting src/importExportFileTest.py _________________ 945s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py'. 945s Hint: make sure your test modules/packages have valid Python names. 945s Traceback: 945s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 945s mod = import_path( 945s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 945s importlib.import_module(module_name) 945s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 945s return _bootstrap._gcd_import(name[level:], package, level) 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s :1387: in _gcd_import 945s ??? 945s :1360: in _find_and_load 945s ??? 945s :1331: in _find_and_load_unlocked 945s ??? 945s :935: in _load_unlocked 945s ??? 945s :1023: in exec_module 945s ??? 945s :488: in _call_with_frames_removed 945s ??? 945s /usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py:30: in 945s from pytest_subtests import SubTests 945s E ModuleNotFoundError: No module named 'pytest_subtests' 945s _________________ ERROR collecting src/jobEncapsulationTest.py _________________ 945s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py'. 945s Hint: make sure your test modules/packages have valid Python names. 945s Traceback: 945s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 945s mod = import_path( 945s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 945s importlib.import_module(module_name) 945s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 945s return _bootstrap._gcd_import(name[level:], package, level) 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s :1387: in _gcd_import 945s ??? 945s :1360: in _find_and_load 945s ??? 945s :1331: in _find_and_load_unlocked 945s ??? 945s :935: in _load_unlocked 945s ??? 945s :1023: in exec_module 945s ??? 945s :488: in _call_with_frames_removed 945s ??? 945s /usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py:17: in 945s from toil.test.src.jobTest import fn1Test 945s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 945s from pytest_subtests import SubTests 945s E ModuleNotFoundError: No module named 'pytest_subtests' 945s _______________________ ERROR collecting src/jobTest.py ________________________ 945s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobTest.py'. 945s Hint: make sure your test modules/packages have valid Python names. 945s Traceback: 945s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 945s mod = import_path( 945s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 945s importlib.import_module(module_name) 945s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 945s return _bootstrap._gcd_import(name[level:], package, level) 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s :1387: in _gcd_import 945s ??? 945s :1360: in _find_and_load 945s ??? 945s :1331: in _find_and_load_unlocked 945s ??? 945s :935: in _load_unlocked 945s ??? 945s :1023: in exec_module 945s ??? 945s :488: in _call_with_frames_removed 945s ??? 945s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 945s from pytest_subtests import SubTests 945s E ModuleNotFoundError: No module named 'pytest_subtests' 945s =================================== FAILURES =================================== 945s __________________________ TestDocker.testDockerClean __________________________ 945s [gw2] linux -- Python 3.13.11 /usr/bin/python3.13 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 945s toil.start(A) 945s ~~~~~~~~~~^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 945s return self._runMainLoop(rootJobDescription) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 945s ).run() 945s ~~~^^ 945s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 945s raise FailedJobsException( 945s ...<3 lines>... 945s ) 945s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v3 945s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v3" follows: 945s =========> 945s [2026-01-30T05:48:18+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:18+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:18+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v1 945s [2026-01-30T05:48:19+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v1 945s [2026-01-30T05:48:19+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 945s apiDockerCall( 945s ~~~~~~~~~~~~~^ 945s job, 945s ^^^^ 945s ...<6 lines>... 945s privileged=True, 945s ^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:19+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 945s result: TResult | None = func() 945s ~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 945s lambda: runtest_hook(item=item, **kwds), 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 945s yield 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 945s return result.get_result() 945s ~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 945s raise exc.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 945s res = yield 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 945s item.runtest() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 945s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 945s result = testfunction(**testargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 945s file_stats = test_file.stat() 945s File "/usr/lib/python3.13/pathlib/_local.py", line 517, in stat 945s return os.stat(self, follow_symlinks=follow_symlinks) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean0/working/test.txt' 945s ----------------------------- Captured stderr call ----------------------------- 945s [2026-01-30T05:48:18+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 1ee1ab1e-aa23-48f0-aa45-d818aa0918ad in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean0/jobstore 945s [2026-01-30T05:48:18+0000] [MainThread] [I] [toil.lib.history] Workflow 1ee1ab1e-aa23-48f0-aa45-d818aa0918ad is a run of 945s [2026-01-30T05:48:18+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:18+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 945s [2026-01-30T05:48:18+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:48:19+0000] [Thread-2 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerCleanFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean0/jobstore kind-_testDockerCleanFn/instance-8h9t8gjf. 945s [2026-01-30T05:48:19+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v1 945s Exit reason: None 945s [2026-01-30T05:48:19+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v2 945s [2026-01-30T05:48:19+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-8h9t8gjf" follows: 945s =========> 945s [2026-01-30T05:48:18+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:18+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:18+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v1 945s [2026-01-30T05:48:19+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v1 945s [2026-01-30T05:48:19+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 945s apiDockerCall( 945s ~~~~~~~~~~~~~^ 945s job, 945s ^^^^ 945s ...<6 lines>... 945s privileged=True, 945s ^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:19+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:48:19+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v2 with ID kind-_testDockerCleanFn/instance-8h9t8gjf to 0 945s [2026-01-30T05:48:19+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 945s [2026-01-30T05:48:19+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v3 is completely failed 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v3 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil.lib.history] Workflow 1ee1ab1e-aa23-48f0-aa45-d818aa0918ad stopped. Success: False 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean0/jobstore) 945s ------------------------------ Captured log call ------------------------------- 945s INFO  toil.lib.history:history.py:369 Recording workflow creation of 1ee1ab1e-aa23-48f0-aa45-d818aa0918ad in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean0/jobstore 945s INFO  toil.lib.history:history.py:399 Workflow 1ee1ab1e-aa23-48f0-aa45-d818aa0918ad is a run of 945s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerCleanFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean0/jobstore kind-_testDockerCleanFn/instance-8h9t8gjf. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v1 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v2 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-8h9t8gjf" follows: 945s =========> 945s [2026-01-30T05:48:18+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:18+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:18+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v1 945s [2026-01-30T05:48:19+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v1 945s [2026-01-30T05:48:19+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 945s apiDockerCall( 945s ~~~~~~~~~~~~~^ 945s job, 945s ^^^^ 945s ...<6 lines>... 945s privileged=True, 945s ^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:19+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v2 with ID kind-_testDockerCleanFn/instance-8h9t8gjf to 0 945s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 945s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v3 is completely failed 945s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 945s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-8h9t8gjf v3 945s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 945s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 945s INFO  toil.lib.history:history.py:530 Workflow 1ee1ab1e-aa23-48f0-aa45-d818aa0918ad stopped. Success: False 945s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean0/jobstore) 945s _____________________ TestDocker.testDockerClean_CRx_FORGO _____________________ 945s [gw2] linux -- Python 3.13.11 /usr/bin/python3.13 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 945s toil.start(A) 945s ~~~~~~~~~~^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 945s return self._runMainLoop(rootJobDescription) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 945s ).run() 945s ~~~^^ 945s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 945s raise FailedJobsException( 945s ...<3 lines>... 945s ) 945s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_FORGO0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v3 945s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v3" follows: 945s =========> 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1 used 1.04x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:23+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 945s apiDockerCall( 945s ~~~~~~~~~~~~~^ 945s job, 945s ^^^^ 945s ...<6 lines>... 945s privileged=True, 945s ^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:23+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 945s result: TResult | None = func() 945s ~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 945s lambda: runtest_hook(item=item, **kwds), 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 945s yield 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 945s return result.get_result() 945s ~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 945s raise exc.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 945s res = yield 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 945s item.runtest() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 945s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 945s result = testfunction(**testargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 133, in testDockerClean_CRx_FORGO 945s self.testDockerClean( 945s ~~~~~~~~~~~~~~~~~~~~^ 945s tmp_path, caching=False, detached=False, rm=True, deferParam=FORGO 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 945s file_stats = test_file.stat() 945s File "/usr/lib/python3.13/pathlib/_local.py", line 517, in stat 945s return os.stat(self, follow_symlinks=follow_symlinks) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_FORGO0/working/test.txt' 945s ----------------------------- Captured stderr call ----------------------------- 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 55591334-c1d0-43c6-bde8-cfd8bd7fd392 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_FORGO0/jobstore 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil.lib.history] Workflow 55591334-c1d0-43c6-bde8-cfd8bd7fd392 is a run of 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:48:23+0000] [Thread-6 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerCleanFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_FORGO0/jobstore kind-_testDockerCleanFn/instance-87p9mbbk. 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1 945s Exit reason: None 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v2 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-87p9mbbk" follows: 945s =========> 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1 used 1.04x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:23+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 945s apiDockerCall( 945s ~~~~~~~~~~~~~^ 945s job, 945s ^^^^ 945s ...<6 lines>... 945s privileged=True, 945s ^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:23+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v2 with ID kind-_testDockerCleanFn/instance-87p9mbbk to 0 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v3 is completely failed 945s [2026-01-30T05:48:24+0000] [Thread-9 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:48:24: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1 used 1.04x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v3 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.lib.history] Workflow 55591334-c1d0-43c6-bde8-cfd8bd7fd392 stopped. Success: False 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_FORGO0/jobstore) 945s ------------------------------ Captured log call ------------------------------- 945s INFO  toil.lib.history:history.py:369 Recording workflow creation of 55591334-c1d0-43c6-bde8-cfd8bd7fd392 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_FORGO0/jobstore 945s INFO  toil.lib.history:history.py:399 Workflow 55591334-c1d0-43c6-bde8-cfd8bd7fd392 is a run of 945s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerCleanFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_FORGO0/jobstore kind-_testDockerCleanFn/instance-87p9mbbk. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v2 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-87p9mbbk" follows: 945s =========> 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1 945s [2026-01-30T05:48:23+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1 used 1.04x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:23+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 945s apiDockerCall( 945s ~~~~~~~~~~~~~^ 945s job, 945s ^^^^ 945s ...<6 lines>... 945s privileged=True, 945s ^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:23+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v2 with ID kind-_testDockerCleanFn/instance-87p9mbbk to 0 945s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 945s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v3 is completely failed 945s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:48:24: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v1 used 1.04x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 945s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-87p9mbbk v3 945s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 945s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 945s INFO  toil.lib.history:history.py:530 Workflow 55591334-c1d0-43c6-bde8-cfd8bd7fd392 stopped. Success: False 945s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_FORGO0/jobstore) 945s _______________________ ToilDocumentationTest.testDocker _______________________ 945s [gw0] linux -- Python 3.13.11 /usr/bin/python3.13 945s Traceback (most recent call last): 945s File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor 945s yield 945s File "/usr/lib/python3.13/unittest/case.py", line 651, in run 945s self._callTestMethod(testMethod) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod 945s if method() is not None: 945s ~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py", line 161, in testDocker 945s self.checkExitCode("tutorial_docker.py") 945s ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py", line 50, in checkExitCode 945s raise RuntimeError(stderr) 945s RuntimeError: [2026-01-30T05:48:21+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of ec00af2f-cf95-4d25-9a16-9a195ee11381 in file:/tmp/tmpxnfw90z1tutorial_docker 945s [2026-01-30T05:48:21+0000] [MainThread] [I] [toil.lib.history] Workflow ec00af2f-cf95-4d25-9a16-9a195ee11381 is a run of /usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py 945s [2026-01-30T05:48:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:21+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 945s [2026-01-30T05:48:21+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:48:22+0000] [Thread-4 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:48:22: Job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v1 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:22+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmpxnfw90z1tutorial_docker kind-apiDockerCall/instance-wj0esx48. 945s [2026-01-30T05:48:22+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v1 945s Exit reason: None 945s [2026-01-30T05:48:22+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v2 945s [2026-01-30T05:48:22+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-wj0esx48" follows: 945s =========> 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v1 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v1) from description 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v1 945s [2026-01-30T05:48:22+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v1 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:22+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:22+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:48:22+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v2 with ID kind-apiDockerCall/instance-wj0esx48 to 1 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:48:23+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmpxnfw90z1tutorial_docker kind-apiDockerCall/instance-wj0esx48. 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v3 945s Exit reason: None 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v5 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-wj0esx48" follows: 945s =========> 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4) from description 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4 945s [2026-01-30T05:48:22+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:22+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:22+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v5 with ID kind-apiDockerCall/instance-wj0esx48 to 0 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.leader] Job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v6 is completely failed 945s [2026-01-30T05:48:23+0000] [Thread-4 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:48:23: Job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:26+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s [2026-01-30T05:48:26+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 945s [2026-01-30T05:48:26+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v6 945s [2026-01-30T05:48:26+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.lib.history] Workflow ec00af2f-cf95-4d25-9a16-9a195ee11381 stopped. Success: False 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/tmpxnfw90z1tutorial_docker) 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py", line 20, in 945s toil.start(align) 945s ~~~~~~~~~~^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 945s return self._runMainLoop(rootJobDescription) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 945s ).run() 945s ~~~^^ 945s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 945s raise FailedJobsException( 945s ...<3 lines>... 945s ) 945s toil.exceptions.FailedJobsException: The job store '/tmp/tmpxnfw90z1tutorial_docker' contains 1 failed jobs: 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v6 945s Log from job "'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v6" follows: 945s =========> 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4) from description 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4 945s [2026-01-30T05:48:22+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:22+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:22+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s 945s ---------------------------- Captured stdout setup ----------------------------- 945s 945s 945s [TEST] toil.test.docs.scriptsTest.ToilDocumentationTest:testDocker (Jan 29 2026 21:48:21:499395 PST) 945s 945s 945s _____________________ TestDocker.testDockerClean_CRx_STOP ______________________ 945s [gw2] linux -- Python 3.13.11 /usr/bin/python3.13 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 945s toil.start(A) 945s ~~~~~~~~~~^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 945s return self._runMainLoop(rootJobDescription) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 945s ).run() 945s ~~~^^ 945s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 945s raise FailedJobsException( 945s ...<3 lines>... 945s ) 945s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_STOP0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v3 945s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v3" follows: 945s =========> 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1 945s [2026-01-30T05:48:28+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1 945s [2026-01-30T05:48:28+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1 used 1.05x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:28+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 945s apiDockerCall( 945s ~~~~~~~~~~~~~^ 945s job, 945s ^^^^ 945s ...<6 lines>... 945s privileged=True, 945s ^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:28+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 945s result: TResult | None = func() 945s ~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 945s lambda: runtest_hook(item=item, **kwds), 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 945s yield 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 945s return result.get_result() 945s ~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 945s raise exc.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 945s res = yield 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 945s item.runtest() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 945s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 945s result = testfunction(**testargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 138, in testDockerClean_CRx_STOP 945s self.testDockerClean( 945s ~~~~~~~~~~~~~~~~~~~~^ 945s tmp_path, caching=False, detached=False, rm=True, deferParam=STOP 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 945s file_stats = test_file.stat() 945s File "/usr/lib/python3.13/pathlib/_local.py", line 517, in stat 945s return os.stat(self, follow_symlinks=follow_symlinks) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_STOP0/working/test.txt' 945s ----------------------------- Captured stderr call ----------------------------- 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 29691c73-955b-4eca-9002-06456faf5cea in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_STOP0/jobstore 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.lib.history] Workflow 29691c73-955b-4eca-9002-06456faf5cea is a run of 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:48:28+0000] [Thread-10 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerCleanFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_STOP0/jobstore kind-_testDockerCleanFn/instance-cac5gp51. 945s [2026-01-30T05:48:28+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1 945s Exit reason: None 945s [2026-01-30T05:48:28+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v2 945s [2026-01-30T05:48:28+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-cac5gp51" follows: 945s =========> 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1 945s [2026-01-30T05:48:28+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1 945s [2026-01-30T05:48:28+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1 used 1.05x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:28+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 945s apiDockerCall( 945s ~~~~~~~~~~~~~^ 945s job, 945s ^^^^ 945s ...<6 lines>... 945s privileged=True, 945s ^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:28+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:48:28+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v2 with ID kind-_testDockerCleanFn/instance-cac5gp51 to 0 945s [2026-01-30T05:48:28+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 945s [2026-01-30T05:48:28+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v3 is completely failed 945s [2026-01-30T05:48:28+0000] [Thread-13 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:48:28: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1 used 1.05x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:31+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s [2026-01-30T05:48:31+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 945s [2026-01-30T05:48:31+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v3 945s [2026-01-30T05:48:31+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 945s [2026-01-30T05:48:32+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 945s [2026-01-30T05:48:32+0000] [MainThread] [I] [toil.lib.history] Workflow 29691c73-955b-4eca-9002-06456faf5cea stopped. Success: False 945s [2026-01-30T05:48:32+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_STOP0/jobstore) 945s ------------------------------ Captured log call ------------------------------- 945s INFO  toil.lib.history:history.py:369 Recording workflow creation of 29691c73-955b-4eca-9002-06456faf5cea in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_STOP0/jobstore 945s INFO  toil.lib.history:history.py:399 Workflow 29691c73-955b-4eca-9002-06456faf5cea is a run of 945s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerCleanFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_STOP0/jobstore kind-_testDockerCleanFn/instance-cac5gp51. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v2 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-cac5gp51" follows: 945s =========> 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1 945s [2026-01-30T05:48:28+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1 945s [2026-01-30T05:48:28+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1 used 1.05x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:28+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 945s apiDockerCall( 945s ~~~~~~~~~~~~~^ 945s job, 945s ^^^^ 945s ...<6 lines>... 945s privileged=True, 945s ^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:28+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v2 with ID kind-_testDockerCleanFn/instance-cac5gp51 to 0 945s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 945s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v3 is completely failed 945s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:48:28: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v1 used 1.05x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 945s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-cac5gp51 v3 945s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 945s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 945s INFO  toil.lib.history:history.py:530 Workflow 29691c73-955b-4eca-9002-06456faf5cea stopped. Success: False 945s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_STOP0/jobstore) 945s ______________________ TestDocker.testDockerClean_CRx_RM _______________________ 945s [gw2] linux -- Python 3.13.11 /usr/bin/python3.13 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 945s toil.start(A) 945s ~~~~~~~~~~^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 945s return self._runMainLoop(rootJobDescription) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 945s ).run() 945s ~~~^^ 945s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 945s raise FailedJobsException( 945s ...<3 lines>... 945s ) 945s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_RM0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v3 945s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v3" follows: 945s =========> 945s [2026-01-30T05:48:32+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:32+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:32+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v1 945s [2026-01-30T05:48:33+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v1 945s [2026-01-30T05:48:33+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 945s apiDockerCall( 945s ~~~~~~~~~~~~~^ 945s job, 945s ^^^^ 945s ...<6 lines>... 945s privileged=True, 945s ^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:33+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 945s result: TResult | None = func() 945s ~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 945s lambda: runtest_hook(item=item, **kwds), 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 945s yield 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 945s return result.get_result() 945s ~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 945s raise exc.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 945s res = yield 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 945s item.runtest() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 945s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 945s result = testfunction(**testargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 143, in testDockerClean_CRx_RM 945s self.testDockerClean( 945s ~~~~~~~~~~~~~~~~~~~~^ 945s tmp_path, caching=False, detached=False, rm=True, deferParam=RM 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 945s file_stats = test_file.stat() 945s File "/usr/lib/python3.13/pathlib/_local.py", line 517, in stat 945s return os.stat(self, follow_symlinks=follow_symlinks) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_RM0/working/test.txt' 945s ----------------------------- Captured stderr call ----------------------------- 945s [2026-01-30T05:48:32+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 1e186032-5dca-429e-8122-7f789cd62a88 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_RM0/jobstore 945s [2026-01-30T05:48:32+0000] [MainThread] [I] [toil.lib.history] Workflow 1e186032-5dca-429e-8122-7f789cd62a88 is a run of 945s [2026-01-30T05:48:32+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:32+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 945s [2026-01-30T05:48:32+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:48:33+0000] [Thread-14 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerCleanFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_RM0/jobstore kind-_testDockerCleanFn/instance-l8k1sato. 945s [2026-01-30T05:48:33+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v1 945s Exit reason: None 945s [2026-01-30T05:48:33+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v2 945s [2026-01-30T05:48:33+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-l8k1sato" follows: 945s =========> 945s [2026-01-30T05:48:32+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:32+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:32+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v1 945s [2026-01-30T05:48:33+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v1 945s [2026-01-30T05:48:33+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 945s apiDockerCall( 945s ~~~~~~~~~~~~~^ 945s job, 945s ^^^^ 945s ...<6 lines>... 945s privileged=True, 945s ^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:33+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:48:33+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v2 with ID kind-_testDockerCleanFn/instance-l8k1sato to 0 945s [2026-01-30T05:48:33+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 945s [2026-01-30T05:48:33+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v3 is completely failed 945s [2026-01-30T05:48:37+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s [2026-01-30T05:48:37+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 945s [2026-01-30T05:48:37+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v3 945s [2026-01-30T05:48:37+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 945s [2026-01-30T05:48:38+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 945s [2026-01-30T05:48:38+0000] [MainThread] [I] [toil.lib.history] Workflow 1e186032-5dca-429e-8122-7f789cd62a88 stopped. Success: False 945s [2026-01-30T05:48:38+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_RM0/jobstore) 945s ------------------------------ Captured log call ------------------------------- 945s INFO  toil.lib.history:history.py:369 Recording workflow creation of 1e186032-5dca-429e-8122-7f789cd62a88 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_RM0/jobstore 945s INFO  toil.lib.history:history.py:399 Workflow 1e186032-5dca-429e-8122-7f789cd62a88 is a run of 945s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerCleanFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_RM0/jobstore kind-_testDockerCleanFn/instance-l8k1sato. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v1 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v2 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-l8k1sato" follows: 945s =========> 945s [2026-01-30T05:48:32+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:32+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:32+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v1 945s [2026-01-30T05:48:33+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v1 945s [2026-01-30T05:48:33+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 945s apiDockerCall( 945s ~~~~~~~~~~~~~^ 945s job, 945s ^^^^ 945s ...<6 lines>... 945s privileged=True, 945s ^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:33+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v2 with ID kind-_testDockerCleanFn/instance-l8k1sato to 0 945s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 945s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v3 is completely failed 945s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 945s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-l8k1sato v3 945s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 945s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 945s INFO  toil.lib.history:history.py:530 Workflow 1e186032-5dca-429e-8122-7f789cd62a88 stopped. Success: False 945s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_RM0/jobstore) 945s ________________________ TestDocker.testDockerPipeChain ________________________ 945s [gw2] linux -- Python 3.13.11 /usr/bin/python3.13 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 945s result: TResult | None = func() 945s ~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 945s lambda: runtest_hook(item=item, **kwds), 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 945s yield 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 945s return result.get_result() 945s ~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 945s raise exc.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 945s res = yield 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 945s item.runtest() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 945s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 945s result = testfunction(**testargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 310, in testDockerPipeChain 945s rv = Job.Runner.startToil(A, options) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 945s return toil.start(job) 945s ~~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 945s return self._runMainLoop(rootJobDescription) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 945s ).run() 945s ~~~^^ 945s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 945s raise FailedJobsException( 945s ...<3 lines>... 945s ) 945s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v6 945s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v6" follows: 945s =========> 945s [2026-01-30T05:48:39+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:39+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:39+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v4 945s [2026-01-30T05:48:40+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v4 945s [2026-01-30T05:48:40+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 945s return apiDockerCall( 945s job, 945s ...<2 lines>... 945s privileged=True, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:40+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s ----------------------------- Captured stderr call ----------------------------- 945s [2026-01-30T05:48:38+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 4e55e42b-d3b3-4442-9899-b394848d9514 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChain0/jobstore 945s [2026-01-30T05:48:38+0000] [MainThread] [I] [toil.lib.history] Workflow 4e55e42b-d3b3-4442-9899-b394848d9514 is a run of 945s [2026-01-30T05:48:38+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:38+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 945s [2026-01-30T05:48:38+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:48:39+0000] [Thread-18 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-md7qxf19. 945s [2026-01-30T05:48:39+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v1 945s Exit reason: None 945s [2026-01-30T05:48:39+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v2 945s [2026-01-30T05:48:39+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-md7qxf19" follows: 945s =========> 945s [2026-01-30T05:48:38+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:38+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:38+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v1 945s [2026-01-30T05:48:38+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v1 945s [2026-01-30T05:48:38+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 945s return apiDockerCall( 945s job, 945s ...<2 lines>... 945s privileged=True, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:38+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:48:39+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v2 with ID kind-_testDockerPipeChainFn/instance-md7qxf19 to 1 945s [2026-01-30T05:48:39+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 945s [2026-01-30T05:48:39+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:48:40+0000] [Thread-18 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-md7qxf19. 945s [2026-01-30T05:48:40+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v3 945s Exit reason: None 945s [2026-01-30T05:48:40+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v5 945s [2026-01-30T05:48:40+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-md7qxf19" follows: 945s =========> 945s [2026-01-30T05:48:39+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:39+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:39+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v4 945s [2026-01-30T05:48:40+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v4 945s [2026-01-30T05:48:40+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 945s return apiDockerCall( 945s job, 945s ...<2 lines>... 945s privileged=True, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:40+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:48:40+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v5 with ID kind-_testDockerPipeChainFn/instance-md7qxf19 to 0 945s [2026-01-30T05:48:40+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v6 is completely failed 945s [2026-01-30T05:48:44+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s [2026-01-30T05:48:44+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 945s [2026-01-30T05:48:44+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v6 945s [2026-01-30T05:48:44+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 945s [2026-01-30T05:48:44+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 945s [2026-01-30T05:48:44+0000] [MainThread] [I] [toil.lib.history] Workflow 4e55e42b-d3b3-4442-9899-b394848d9514 stopped. Success: False 945s [2026-01-30T05:48:44+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChain0/jobstore) 945s ------------------------------ Captured log call ------------------------------- 945s INFO  toil.lib.history:history.py:369 Recording workflow creation of 4e55e42b-d3b3-4442-9899-b394848d9514 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChain0/jobstore 945s INFO  toil.lib.history:history.py:399 Workflow 4e55e42b-d3b3-4442-9899-b394848d9514 is a run of 945s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-md7qxf19. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v1 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v2 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-md7qxf19" follows: 945s =========> 945s [2026-01-30T05:48:38+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:38+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:38+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v1 945s [2026-01-30T05:48:38+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v1 945s [2026-01-30T05:48:38+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 945s return apiDockerCall( 945s job, 945s ...<2 lines>... 945s privileged=True, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:38+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v2 with ID kind-_testDockerPipeChainFn/instance-md7qxf19 to 1 945s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-md7qxf19. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v3 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v5 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-md7qxf19" follows: 945s =========> 945s [2026-01-30T05:48:39+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:39+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:39+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v4 945s [2026-01-30T05:48:40+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v4 945s [2026-01-30T05:48:40+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 945s return apiDockerCall( 945s job, 945s ...<2 lines>... 945s privileged=True, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:40+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v5 with ID kind-_testDockerPipeChainFn/instance-md7qxf19 to 0 945s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v6 is completely failed 945s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 945s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v6 945s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 945s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 945s INFO  toil.lib.history:history.py:530 Workflow 4e55e42b-d3b3-4442-9899-b394848d9514 stopped. Success: False 945s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChain0/jobstore) 945s _________________ TestDocker.testDockerPipeChainErrorDetection _________________ 945s [gw2] linux -- Python 3.13.11 /usr/bin/python3.13 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 945s result: TResult | None = func() 945s ~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 945s lambda: runtest_hook(item=item, **kwds), 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 945s yield 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 945s return result.get_result() 945s ~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 945s raise exc.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 945s res = yield 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 945s item.runtest() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 945s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 945s result = testfunction(**testargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 332, in testDockerPipeChainErrorDetection 945s rv = Job.Runner.startToil(A, options) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 945s return toil.start(job) 945s ~~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 945s return self._runMainLoop(rootJobDescription) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 945s ).run() 945s ~~~^^ 945s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 945s raise FailedJobsException( 945s ...<3 lines>... 945s ) 945s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChainErrorDetect0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v6 945s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v6" follows: 945s =========> 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4 945s [2026-01-30T05:48:46+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4 945s [2026-01-30T05:48:46+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:46+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 945s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 945s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:46+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s ----------------------------- Captured stderr call ----------------------------- 945s [2026-01-30T05:48:44+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 52d3c5a9-8bfe-430e-8536-cd5675620f45 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChainErrorDetect0/jobstore 945s [2026-01-30T05:48:44+0000] [MainThread] [I] [toil.lib.history] Workflow 52d3c5a9-8bfe-430e-8536-cd5675620f45 is a run of 945s [2026-01-30T05:48:44+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:44+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 945s [2026-01-30T05:48:44+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:48:45+0000] [Thread-22 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainErrorFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-0zhordoo. 945s [2026-01-30T05:48:45+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v1 945s Exit reason: None 945s [2026-01-30T05:48:45+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v2 945s [2026-01-30T05:48:45+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-0zhordoo" follows: 945s =========> 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v1 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v1 945s [2026-01-30T05:48:45+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:45+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 945s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 945s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:45+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:48:45+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v2 with ID kind-_testDockerPipeChainErrorFn/instance-0zhordoo to 1 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:48:45+0000] [Thread-25 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:48:45: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:46+0000] [Thread-25 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:48:46: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:46+0000] [Thread-22 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainErrorFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-0zhordoo. 945s [2026-01-30T05:48:46+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v3 945s Exit reason: None 945s [2026-01-30T05:48:46+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v5 945s [2026-01-30T05:48:46+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-0zhordoo" follows: 945s =========> 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4 945s [2026-01-30T05:48:46+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4 945s [2026-01-30T05:48:46+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:46+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 945s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 945s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:46+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:48:46+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v5 with ID kind-_testDockerPipeChainErrorFn/instance-0zhordoo to 0 945s [2026-01-30T05:48:46+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v6 is completely failed 945s [2026-01-30T05:48:49+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s [2026-01-30T05:48:49+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 945s [2026-01-30T05:48:49+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v6 945s [2026-01-30T05:48:49+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 945s [2026-01-30T05:48:49+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 945s [2026-01-30T05:48:49+0000] [MainThread] [I] [toil.lib.history] Workflow 52d3c5a9-8bfe-430e-8536-cd5675620f45 stopped. Success: False 945s [2026-01-30T05:48:49+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChainErrorDetect0/jobstore) 945s ------------------------------ Captured log call ------------------------------- 945s INFO  toil.lib.history:history.py:369 Recording workflow creation of 52d3c5a9-8bfe-430e-8536-cd5675620f45 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChainErrorDetect0/jobstore 945s INFO  toil.lib.history:history.py:399 Workflow 52d3c5a9-8bfe-430e-8536-cd5675620f45 is a run of 945s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainErrorFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-0zhordoo. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v1 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v2 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-0zhordoo" follows: 945s =========> 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v1 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v1 945s [2026-01-30T05:48:45+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:45+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 945s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 945s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:45+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v2 with ID kind-_testDockerPipeChainErrorFn/instance-0zhordoo to 1 945s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:48:45: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:48:46: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainErrorFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-0zhordoo. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v3 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v5 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-0zhordoo" follows: 945s =========> 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4 945s [2026-01-30T05:48:46+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4 945s [2026-01-30T05:48:46+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:46+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 945s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 945s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:46+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v5 with ID kind-_testDockerPipeChainErrorFn/instance-0zhordoo to 0 945s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v6 is completely failed 945s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 945s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v6 945s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 945s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 945s INFO  toil.lib.history:history.py:530 Workflow 52d3c5a9-8bfe-430e-8536-cd5675620f45 stopped. Success: False 945s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChainErrorDetect0/jobstore) 945s _____________________ TestDocker.testNonCachingDockerChain _____________________ 945s [gw2] linux -- Python 3.13.11 /usr/bin/python3.13 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 945s result: TResult | None = func() 945s ~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 945s lambda: runtest_hook(item=item, **kwds), 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 945s yield 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 945s return result.get_result() 945s ~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 945s raise exc.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 945s res = yield 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 945s item.runtest() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 945s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 945s result = testfunction(**testargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 336, in testNonCachingDockerChain 945s self.testDockerPipeChain(tmp_path, caching=True) 945s ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 310, in testDockerPipeChain 945s rv = Job.Runner.startToil(A, options) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 945s return toil.start(job) 945s ~~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 945s return self._runMainLoop(rootJobDescription) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 945s ).run() 945s ~~~^^ 945s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 945s raise FailedJobsException( 945s ...<3 lines>... 945s ) 945s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v6 945s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v6" follows: 945s =========> 945s [2026-01-30T05:48:51+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:51+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:51+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4 945s [2026-01-30T05:48:51+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4 945s [2026-01-30T05:48:51+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:51+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 945s return apiDockerCall( 945s job, 945s ...<2 lines>... 945s privileged=True, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:51+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s ----------------------------- Captured stderr call ----------------------------- 945s [2026-01-30T05:48:49+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of eefb84c1-4271-4703-b34b-bddc44db0b00 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChain0/jobstore 945s [2026-01-30T05:48:49+0000] [MainThread] [I] [toil.lib.history] Workflow eefb84c1-4271-4703-b34b-bddc44db0b00 is a run of 945s [2026-01-30T05:48:49+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:49+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 945s [2026-01-30T05:48:49+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:48:50+0000] [Thread-26 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-w7daaumv. 945s [2026-01-30T05:48:50+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v1 945s Exit reason: None 945s [2026-01-30T05:48:50+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v2 945s [2026-01-30T05:48:50+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-w7daaumv" follows: 945s =========> 945s [2026-01-30T05:48:50+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:50+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:50+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v1 945s [2026-01-30T05:48:50+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v1 945s [2026-01-30T05:48:50+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:50+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 945s return apiDockerCall( 945s job, 945s ...<2 lines>... 945s privileged=True, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:50+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:48:50+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v2 with ID kind-_testDockerPipeChainFn/instance-w7daaumv to 1 945s [2026-01-30T05:48:50+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 945s [2026-01-30T05:48:50+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:48:50+0000] [Thread-29 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:48:50: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:51+0000] [Thread-29 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:48:51: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:51+0000] [Thread-26 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-w7daaumv. 945s [2026-01-30T05:48:51+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v3 945s Exit reason: None 945s [2026-01-30T05:48:51+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v5 945s [2026-01-30T05:48:51+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-w7daaumv" follows: 945s =========> 945s [2026-01-30T05:48:51+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:51+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:51+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4 945s [2026-01-30T05:48:51+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4 945s [2026-01-30T05:48:51+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:51+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 945s return apiDockerCall( 945s job, 945s ...<2 lines>... 945s privileged=True, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:51+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:48:51+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v5 with ID kind-_testDockerPipeChainFn/instance-w7daaumv to 0 945s [2026-01-30T05:48:51+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v6 is completely failed 945s [2026-01-30T05:48:54+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s [2026-01-30T05:48:54+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 945s [2026-01-30T05:48:54+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v6 945s [2026-01-30T05:48:54+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 945s [2026-01-30T05:48:55+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 945s [2026-01-30T05:48:55+0000] [MainThread] [I] [toil.lib.history] Workflow eefb84c1-4271-4703-b34b-bddc44db0b00 stopped. Success: False 945s [2026-01-30T05:48:55+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChain0/jobstore) 945s ------------------------------ Captured log call ------------------------------- 945s INFO  toil.lib.history:history.py:369 Recording workflow creation of eefb84c1-4271-4703-b34b-bddc44db0b00 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChain0/jobstore 945s INFO  toil.lib.history:history.py:399 Workflow eefb84c1-4271-4703-b34b-bddc44db0b00 is a run of 945s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-w7daaumv. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v1 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v2 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-w7daaumv" follows: 945s =========> 945s [2026-01-30T05:48:50+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:50+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:50+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v1 945s [2026-01-30T05:48:50+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v1 945s [2026-01-30T05:48:50+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:50+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 945s return apiDockerCall( 945s job, 945s ...<2 lines>... 945s privileged=True, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:50+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v2 with ID kind-_testDockerPipeChainFn/instance-w7daaumv to 1 945s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:48:50: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:48:51: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-w7daaumv. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v3 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v5 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-w7daaumv" follows: 945s =========> 945s [2026-01-30T05:48:51+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:51+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:51+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4 945s [2026-01-30T05:48:51+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4 945s [2026-01-30T05:48:51+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:51+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 945s return apiDockerCall( 945s job, 945s ...<2 lines>... 945s privileged=True, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:51+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v5 with ID kind-_testDockerPipeChainFn/instance-w7daaumv to 0 945s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v6 is completely failed 945s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 945s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v6 945s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 945s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 945s INFO  toil.lib.history:history.py:530 Workflow eefb84c1-4271-4703-b34b-bddc44db0b00 stopped. Success: False 945s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChain0/jobstore) 945s ______________ TestDocker.testNonCachingDockerChainErrorDetection ______________ 945s [gw2] linux -- Python 3.13.11 /usr/bin/python3.13 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 945s result: TResult | None = func() 945s ~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 945s lambda: runtest_hook(item=item, **kwds), 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 945s yield 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 945s return result.get_result() 945s ~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 945s raise exc.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 945s res = yield 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 945s item.runtest() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 945s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 945s result = testfunction(**testargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 339, in testNonCachingDockerChainErrorDetection 945s self.testDockerPipeChainErrorDetection(tmp_path, caching=True) 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 332, in testDockerPipeChainErrorDetection 945s rv = Job.Runner.startToil(A, options) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 945s return toil.start(job) 945s ~~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 945s return self._runMainLoop(rootJobDescription) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 945s ).run() 945s ~~~^^ 945s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 945s raise FailedJobsException( 945s ...<3 lines>... 945s ) 945s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChainError0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v6 945s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v6" follows: 945s =========> 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4 945s [2026-01-30T05:48:56+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:56+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 945s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 945s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:56+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s ----------------------------- Captured stderr call ----------------------------- 945s [2026-01-30T05:48:55+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of d119bad4-7706-445f-a120-0091d2297394 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChainError0/jobstore 945s [2026-01-30T05:48:55+0000] [MainThread] [I] [toil.lib.history] Workflow d119bad4-7706-445f-a120-0091d2297394 is a run of 945s [2026-01-30T05:48:55+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:55+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 945s [2026-01-30T05:48:55+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:48:56+0000] [Thread-30 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainErrorFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-bb7e9btz. 945s [2026-01-30T05:48:56+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v1 945s Exit reason: None 945s [2026-01-30T05:48:56+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v2 945s [2026-01-30T05:48:56+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-bb7e9btz" follows: 945s =========> 945s [2026-01-30T05:48:55+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:55+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:55+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v1 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v1 945s [2026-01-30T05:48:56+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:56+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 945s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 945s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:56+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:48:56+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v2 with ID kind-_testDockerPipeChainErrorFn/instance-bb7e9btz to 1 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:48:56+0000] [Thread-33 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:48:56: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:57+0000] [Thread-33 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:48:57: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:57+0000] [Thread-30 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainErrorFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-bb7e9btz. 945s [2026-01-30T05:48:57+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v3 945s Exit reason: None 945s [2026-01-30T05:48:57+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v5 945s [2026-01-30T05:48:57+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-bb7e9btz" follows: 945s =========> 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4 945s [2026-01-30T05:48:56+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:56+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 945s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 945s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:56+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:48:57+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v5 with ID kind-_testDockerPipeChainErrorFn/instance-bb7e9btz to 0 945s [2026-01-30T05:48:57+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v6 is completely failed 945s [2026-01-30T05:49:00+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s [2026-01-30T05:49:00+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 945s [2026-01-30T05:49:00+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v6 945s [2026-01-30T05:49:00+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 945s [2026-01-30T05:49:01+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 945s [2026-01-30T05:49:01+0000] [MainThread] [I] [toil.lib.history] Workflow d119bad4-7706-445f-a120-0091d2297394 stopped. Success: False 945s [2026-01-30T05:49:01+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChainError0/jobstore) 945s ------------------------------ Captured log call ------------------------------- 945s INFO  toil.lib.history:history.py:369 Recording workflow creation of d119bad4-7706-445f-a120-0091d2297394 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChainError0/jobstore 945s INFO  toil.lib.history:history.py:399 Workflow d119bad4-7706-445f-a120-0091d2297394 is a run of 945s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainErrorFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-bb7e9btz. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v1 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v2 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-bb7e9btz" follows: 945s =========> 945s [2026-01-30T05:48:55+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:55+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:55+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v1 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v1 945s [2026-01-30T05:48:56+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:56+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 945s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 945s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:56+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v2 with ID kind-_testDockerPipeChainErrorFn/instance-bb7e9btz to 1 945s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:48:56: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:48:57: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerPipeChainErrorFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-bb7e9btz. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v3 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v5 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-bb7e9btz" follows: 945s =========> 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4 945s [2026-01-30T05:48:56+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:56+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 945s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 945s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:56+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v5 with ID kind-_testDockerPipeChainErrorFn/instance-bb7e9btz to 0 945s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v6 is completely failed 945s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 945s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v6 945s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 945s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 945s INFO  toil.lib.history:history.py:530 Workflow d119bad4-7706-445f-a120-0091d2297394 stopped. Success: False 945s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChainError0/jobstore) 945s __________________________ TestDocker.testDockerLogs ___________________________ 945s [gw2] linux -- Python 3.13.11 /usr/bin/python3.13 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 945s result: TResult | None = func() 945s ~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 945s lambda: runtest_hook(item=item, **kwds), 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 945s yield 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 945s return result.get_result() 945s ~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 945s raise exc.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 945s res = yield 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 945s item.runtest() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 945s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 945s result = testfunction(**testargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 945s rv = Job.Runner.startToil(A, options) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 945s return toil.start(job) 945s ~~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 945s return self._runMainLoop(rootJobDescription) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 945s ).run() 945s ~~~^^ 945s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 945s raise FailedJobsException( 945s ...<3 lines>... 945s ) 945s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v6 945s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v6" follows: 945s =========> 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4 945s [2026-01-30T05:49:04+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:04+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:04+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s ----------------------------- Captured stderr call ----------------------------- 945s [2026-01-30T05:49:01+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 300a2414-7363-49ed-a7e3-516cd997c747 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs0/jobstore 945s [2026-01-30T05:49:01+0000] [MainThread] [I] [toil.lib.history] Workflow 300a2414-7363-49ed-a7e3-516cd997c747 is a run of 945s [2026-01-30T05:49:01+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:01+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 945s [2026-01-30T05:49:01+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:49:03+0000] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run 945s [2026-01-30T05:49:04+0000] [Thread-34 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-_iuhiz43. 945s [2026-01-30T05:49:04+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v1 945s Exit reason: None 945s [2026-01-30T05:49:04+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v2 945s [2026-01-30T05:49:04+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-_iuhiz43" follows: 945s =========> 945s [2026-01-30T05:49:03+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:03+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:03+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v1 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v1 945s [2026-01-30T05:49:04+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:04+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:04+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:49:04+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v2 with ID kind-_testDockerLogsFn/instance-_iuhiz43 to 1 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:49:04+0000] [Thread-37 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:49:04: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:05+0000] [Thread-37 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:49:05: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:05+0000] [Thread-34 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-_iuhiz43. 945s [2026-01-30T05:49:05+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v3 945s Exit reason: None 945s [2026-01-30T05:49:05+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v5 945s [2026-01-30T05:49:05+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-_iuhiz43" follows: 945s =========> 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4 945s [2026-01-30T05:49:04+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:04+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:04+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:49:05+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v5 with ID kind-_testDockerLogsFn/instance-_iuhiz43 to 0 945s [2026-01-30T05:49:05+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v6 is completely failed 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v6 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil.lib.history] Workflow 300a2414-7363-49ed-a7e3-516cd997c747 stopped. Success: False 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs0/jobstore) 945s ------------------------------ Captured log call ------------------------------- 945s INFO  toil.lib.history:history.py:369 Recording workflow creation of 300a2414-7363-49ed-a7e3-516cd997c747 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs0/jobstore 945s INFO  toil.lib.history:history.py:399 Workflow 300a2414-7363-49ed-a7e3-516cd997c747 is a run of 945s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s INFO  toil.leader:leader.py:1231 1 jobs are running, 0 jobs are issued and waiting to run 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-_iuhiz43. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v1 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v2 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-_iuhiz43" follows: 945s =========> 945s [2026-01-30T05:49:03+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:03+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:03+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v1 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v1 945s [2026-01-30T05:49:04+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:04+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:04+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v2 with ID kind-_testDockerLogsFn/instance-_iuhiz43 to 1 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:49:04: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v1 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:49:05: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-_iuhiz43. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v3 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v5 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-_iuhiz43" follows: 945s =========> 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4 945s [2026-01-30T05:49:04+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:04+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:04+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v5 with ID kind-_testDockerLogsFn/instance-_iuhiz43 to 0 945s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v6 is completely failed 945s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 945s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v6 945s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 945s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 945s INFO  toil.lib.history:history.py:530 Workflow 300a2414-7363-49ed-a7e3-516cd997c747 stopped. Success: False 945s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs0/jobstore) 945s _______________________ TestDocker.testDockerLogs_Stream _______________________ 945s [gw2] linux -- Python 3.13.11 /usr/bin/python3.13 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 945s result: TResult | None = func() 945s ~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 945s lambda: runtest_hook(item=item, **kwds), 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 945s yield 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 945s return result.get_result() 945s ~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 945s raise exc.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 945s res = yield 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 945s item.runtest() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 945s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 945s result = testfunction(**testargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 366, in testDockerLogs_Stream 945s self.testDockerLogs(tmp_path, stream=True, demux=False) 945s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 945s rv = Job.Runner.startToil(A, options) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 945s return toil.start(job) 945s ~~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 945s return self._runMainLoop(rootJobDescription) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 945s ).run() 945s ~~~^^ 945s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 945s raise FailedJobsException( 945s ...<3 lines>... 945s ) 945s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v6 945s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v6" follows: 945s =========> 945s [2026-01-30T05:49:10+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:10+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:10+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4 945s [2026-01-30T05:49:11+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4 945s [2026-01-30T05:49:11+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:11+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:11+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s ----------------------------- Captured stderr call ----------------------------- 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 2a6580d6-0979-4a67-a11c-2964d7f85b1d in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Stream0/jobstore 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil.lib.history] Workflow 2a6580d6-0979-4a67-a11c-2964d7f85b1d is a run of 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:49:10+0000] [Thread-38 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-_0gxyjha. 945s [2026-01-30T05:49:10+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v1 945s Exit reason: None 945s [2026-01-30T05:49:10+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v2 945s [2026-01-30T05:49:10+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-_0gxyjha" follows: 945s =========> 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v1 945s [2026-01-30T05:49:10+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v1 945s [2026-01-30T05:49:10+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v1 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:10+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:10+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:49:10+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v2 with ID kind-_testDockerLogsFn/instance-_0gxyjha to 1 945s [2026-01-30T05:49:10+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 945s [2026-01-30T05:49:10+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:49:10+0000] [Thread-41 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:49:10: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v1 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:11+0000] [Thread-38 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-_0gxyjha. 945s [2026-01-30T05:49:11+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v3 945s Exit reason: None 945s [2026-01-30T05:49:11+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v5 945s [2026-01-30T05:49:11+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-_0gxyjha" follows: 945s =========> 945s [2026-01-30T05:49:10+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:10+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:10+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4 945s [2026-01-30T05:49:11+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4 945s [2026-01-30T05:49:11+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:11+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:11+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:49:11+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v5 with ID kind-_testDockerLogsFn/instance-_0gxyjha to 0 945s [2026-01-30T05:49:11+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v6 is completely failed 945s [2026-01-30T05:49:11+0000] [Thread-41 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:49:11: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:14+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s [2026-01-30T05:49:14+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 945s [2026-01-30T05:49:14+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v6 945s [2026-01-30T05:49:14+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 945s [2026-01-30T05:49:15+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 945s [2026-01-30T05:49:15+0000] [MainThread] [I] [toil.lib.history] Workflow 2a6580d6-0979-4a67-a11c-2964d7f85b1d stopped. Success: False 945s [2026-01-30T05:49:15+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Stream0/jobstore) 945s ------------------------------ Captured log call ------------------------------- 945s INFO  toil.lib.history:history.py:369 Recording workflow creation of 2a6580d6-0979-4a67-a11c-2964d7f85b1d in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Stream0/jobstore 945s INFO  toil.lib.history:history.py:399 Workflow 2a6580d6-0979-4a67-a11c-2964d7f85b1d is a run of 945s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-_0gxyjha. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v1 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v2 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-_0gxyjha" follows: 945s =========> 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:09+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v1 945s [2026-01-30T05:49:10+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v1 945s [2026-01-30T05:49:10+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v1 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:10+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:10+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v2 with ID kind-_testDockerLogsFn/instance-_0gxyjha to 1 945s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:49:10: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v1 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-_0gxyjha. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v3 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v5 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-_0gxyjha" follows: 945s =========> 945s [2026-01-30T05:49:10+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:10+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:10+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4 945s [2026-01-30T05:49:11+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4 945s [2026-01-30T05:49:11+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:11+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:11+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v5 with ID kind-_testDockerLogsFn/instance-_0gxyjha to 0 945s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v6 is completely failed 945s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:49:11: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 945s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v6 945s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 945s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 945s INFO  toil.lib.history:history.py:530 Workflow 2a6580d6-0979-4a67-a11c-2964d7f85b1d stopped. Success: False 945s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Stream0/jobstore) 945s _______________________ TestDocker.testDockerLogs_Demux ________________________ 945s [gw2] linux -- Python 3.13.11 /usr/bin/python3.13 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 945s result: TResult | None = func() 945s ~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 945s lambda: runtest_hook(item=item, **kwds), 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 945s yield 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 945s return result.get_result() 945s ~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 945s raise exc.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 945s res = yield 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 945s item.runtest() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 945s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 945s result = testfunction(**testargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 369, in testDockerLogs_Demux 945s self.testDockerLogs(tmp_path, stream=False, demux=True) 945s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 945s rv = Job.Runner.startToil(A, options) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 945s return toil.start(job) 945s ~~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 945s return self._runMainLoop(rootJobDescription) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 945s ).run() 945s ~~~^^ 945s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 945s raise FailedJobsException( 945s ...<3 lines>... 945s ) 945s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v6 945s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v6" follows: 945s =========> 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4 945s [2026-01-30T05:49:16+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:16+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:16+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s ----------------------------- Captured stderr call ----------------------------- 945s [2026-01-30T05:49:15+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 9208cb74-14ed-43bd-afcf-6757347446b0 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux0/jobstore 945s [2026-01-30T05:49:15+0000] [MainThread] [I] [toil.lib.history] Workflow 9208cb74-14ed-43bd-afcf-6757347446b0 is a run of 945s [2026-01-30T05:49:15+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:15+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 945s [2026-01-30T05:49:15+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:49:16+0000] [Thread-42 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-233c3gcg. 945s [2026-01-30T05:49:16+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v1 945s Exit reason: None 945s [2026-01-30T05:49:16+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v2 945s [2026-01-30T05:49:16+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-233c3gcg" follows: 945s =========> 945s [2026-01-30T05:49:15+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:15+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:15+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v1 945s [2026-01-30T05:49:15+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v1 945s [2026-01-30T05:49:15+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:15+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:15+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:49:16+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v2 with ID kind-_testDockerLogsFn/instance-233c3gcg to 1 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:49:16+0000] [Thread-45 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:49:16: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:16+0000] [Thread-42 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-233c3gcg. 945s [2026-01-30T05:49:16+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v3 945s Exit reason: None 945s [2026-01-30T05:49:16+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v5 945s [2026-01-30T05:49:16+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-233c3gcg" follows: 945s =========> 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4 945s [2026-01-30T05:49:16+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:16+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:16+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:49:16+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v5 with ID kind-_testDockerLogsFn/instance-233c3gcg to 0 945s [2026-01-30T05:49:16+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v6 is completely failed 945s [2026-01-30T05:49:17+0000] [Thread-45 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:49:17: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v6 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil.lib.history] Workflow 9208cb74-14ed-43bd-afcf-6757347446b0 stopped. Success: False 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux0/jobstore) 945s ------------------------------ Captured log call ------------------------------- 945s INFO  toil.lib.history:history.py:369 Recording workflow creation of 9208cb74-14ed-43bd-afcf-6757347446b0 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux0/jobstore 945s INFO  toil.lib.history:history.py:399 Workflow 9208cb74-14ed-43bd-afcf-6757347446b0 is a run of 945s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-233c3gcg. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v1 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v2 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-233c3gcg" follows: 945s =========> 945s [2026-01-30T05:49:15+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:15+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:15+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v1 945s [2026-01-30T05:49:15+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v1 945s [2026-01-30T05:49:15+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:15+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:15+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v2 with ID kind-_testDockerLogsFn/instance-233c3gcg to 1 945s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:49:16: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-233c3gcg. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v3 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v5 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-233c3gcg" follows: 945s =========> 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4 945s [2026-01-30T05:49:16+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:16+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:16+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v5 with ID kind-_testDockerLogsFn/instance-233c3gcg to 0 945s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v6 is completely failed 945s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:49:17: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 945s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v6 945s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 945s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 945s INFO  toil.lib.history:history.py:530 Workflow 9208cb74-14ed-43bd-afcf-6757347446b0 stopped. Success: False 945s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux0/jobstore) 945s ____________________ TestDocker.testDockerLogs_Demux_Stream ____________________ 945s [gw2] linux -- Python 3.13.11 /usr/bin/python3.13 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 945s result: TResult | None = func() 945s ~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 945s lambda: runtest_hook(item=item, **kwds), 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 945s yield 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 945s return result.get_result() 945s ~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 945s raise exc.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 945s res = yield 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 945s teardown.throw(exception) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 945s return (yield) 945s ^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 945s item.runtest() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 945s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 945s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 945s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 945s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 945s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 945s raise exception 945s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 945s res = hook_impl.function(*args) 945s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 945s result = testfunction(**testargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 372, in testDockerLogs_Demux_Stream 945s self.testDockerLogs(tmp_path, stream=True, demux=True) 945s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 945s rv = Job.Runner.startToil(A, options) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 945s return toil.start(job) 945s ~~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 945s return self._runMainLoop(rootJobDescription) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 945s ).run() 945s ~~~^^ 945s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 945s raise FailedJobsException( 945s ...<3 lines>... 945s ) 945s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v6 945s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v6" follows: 945s =========> 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4 945s [2026-01-30T05:49:21+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:21+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:21+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s ----------------------------- Captured stderr call ----------------------------- 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of f6433220-c00f-416c-bd52-71fe8d539cbc in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux_Stream0/jobstore 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil.lib.history] Workflow f6433220-c00f-416c-bd52-71fe8d539cbc is a run of 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:49:21+0000] [Thread-46 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-dzk5e2nl. 945s [2026-01-30T05:49:21+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v1 945s Exit reason: None 945s [2026-01-30T05:49:21+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v2 945s [2026-01-30T05:49:21+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-dzk5e2nl" follows: 945s =========> 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v1 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v1 945s [2026-01-30T05:49:20+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:20+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:20+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:49:21+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v2 with ID kind-_testDockerLogsFn/instance-dzk5e2nl to 1 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:49:21+0000] [Thread-49 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:49:21: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:22+0000] [Thread-46 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-dzk5e2nl. 945s [2026-01-30T05:49:22+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v3 945s Exit reason: None 945s [2026-01-30T05:49:22+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v5 945s [2026-01-30T05:49:22+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-dzk5e2nl" follows: 945s =========> 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4 945s [2026-01-30T05:49:21+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:21+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:21+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:49:22+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v5 with ID kind-_testDockerLogsFn/instance-dzk5e2nl to 0 945s [2026-01-30T05:49:22+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v6 is completely failed 945s [2026-01-30T05:49:22+0000] [Thread-49 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:49:22: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:25+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s [2026-01-30T05:49:25+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 945s [2026-01-30T05:49:25+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v6 945s [2026-01-30T05:49:25+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 945s [2026-01-30T05:49:25+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 945s [2026-01-30T05:49:25+0000] [MainThread] [I] [toil.lib.history] Workflow f6433220-c00f-416c-bd52-71fe8d539cbc stopped. Success: False 945s [2026-01-30T05:49:25+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux_Stream0/jobstore) 945s ------------------------------ Captured log call ------------------------------- 945s INFO  toil.lib.history:history.py:369 Recording workflow creation of f6433220-c00f-416c-bd52-71fe8d539cbc in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux_Stream0/jobstore 945s INFO  toil.lib.history:history.py:399 Workflow f6433220-c00f-416c-bd52-71fe8d539cbc is a run of 945s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-dzk5e2nl. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v1 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v2 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-dzk5e2nl" follows: 945s =========> 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v1 945s [2026-01-30T05:49:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v1 945s [2026-01-30T05:49:20+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:20+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:20+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v2 with ID kind-_testDockerLogsFn/instance-dzk5e2nl to 1 945s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 945s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:49:21: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v1 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s ERROR  toil.batchSystems.singleMachine:singleMachine.py:864 Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-dzk5e2nl. 945s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v3 945s Exit reason: None 945s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v5 945s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-dzk5e2nl" follows: 945s =========> 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4 945s [2026-01-30T05:49:21+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:21+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:21+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v5 with ID kind-_testDockerLogsFn/instance-dzk5e2nl to 0 945s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v6 is completely failed 945s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 05:49:22: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 945s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v6 945s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 945s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 945s INFO  toil.lib.history:history.py:530 Workflow f6433220-c00f-416c-bd52-71fe8d539cbc stopped. Success: False 945s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux_Stream0/jobstore) 945s =========================== short test summary info ============================ 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:603: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:603: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:217: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:217: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:189: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:189: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1115: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1127: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:621: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1115: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1127: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:825: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:621: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:800: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:825: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:151: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:800: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:160: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:151: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:313: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:160: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:202: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:313: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1079: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:202: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1467: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1446: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:450: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:238: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1079: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:421: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:450: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:238: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:405: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:421: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:405: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:380: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:380: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:529: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:529: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:264: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:264: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:585: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:585: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:960: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:960: Configure AWS credentials to include this test. 945s SKIPPED [13] ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py:1139: Configure AWS credentials to include this test. 945s SKIPPED [13] ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py:1139: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:32: Consumes unauthenticated Docker Hub pulls if run 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:38: Consumes unauthenticated Docker Hub pulls if run 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:45: Consumes unauthenticated Docker Hub pulls if run 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:26: Consumes unauthenticated Docker Hub pulls if run 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:731: Install Toil with the 'server' extra to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:646: Install Toil with the 'server' extra to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:697: Install Toil with the 'server' extra to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:706: Install Toil with the 'server' extra to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:685: Install Toil with the 'server' extra to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:676: Install Toil with the 'server' extra to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:721: Install Toil with the 'server' extra to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:619: Install Toil with the 'server' extra to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:600: Install Toil with the 'server' extra to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:668: Install Toil with the 'server' extra to include this test. 945s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:731: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 945s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:646: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 945s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:697: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 945s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:706: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 945s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:685: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 945s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:676: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 945s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:721: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 945s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:619: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 945s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:600: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 945s SKIPPED [2] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:668: Set TOIL_WES_BROKER_URL to a URL to a RabbitMQ broker for Celery to include this test. 945s SKIPPED [7] ../../../../usr/lib/python3/dist-packages/_pytest/unittest.py:498: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:373: Set TOIL_AWS_KEYNAME to an AWS-stored SSH key to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:409: Set TOIL_AWS_KEYNAME to an AWS-stored SSH key to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:122: Set TOIL_AWS_KEYNAME to an AWS-stored SSH key to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:343: Set TOIL_AWS_KEYNAME to an AWS-stored SSH key to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:297: Set TOIL_AWS_KEYNAME to an AWS-stored SSH key to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:373: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:409: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:122: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:343: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py:297: Set TOIL_GOOGLE_PROJECTID to a Google project ID to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:541: Install Toil with the 'server' extra to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:535: Install Toil with the 'server' extra to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:526: Install Toil with the 'server' extra to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py:533: Install Mesos (and Toil with the 'mesos' extra) to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:123: Install Mesos (and Toil with the 'mesos' extra) to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:147: Install Mesos (and Toil with the 'mesos' extra) to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py:255: Install Toil with the 'wdl' extra to include this test. 945s SKIPPED [3] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:96: Install Toil with the 'server' extra to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:245: Install Toil with the 'server' extra to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1568: Configure AWS credentials to include this test. 945s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:48: Install Toil with the 'server' extra to include this test. 945s FAILED lib/dockerTest.py::TestDocker::testDockerClean - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean0/working/test.txt' 945s FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_FORGO - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_FORGO0/working/test.txt' 945s FAILED docs/scriptsTest.py::ToilDocumentationTest::testDocker - RuntimeError: [2026-01-30T05:48:21+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of ec00af2f-cf95-4d25-9a16-9a195ee11381 in file:/tmp/tmpxnfw90z1tutorial_docker 945s [2026-01-30T05:48:21+0000] [MainThread] [I] [toil.lib.history] Workflow ec00af2f-cf95-4d25-9a16-9a195ee11381 is a run of /usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py 945s [2026-01-30T05:48:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:21+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 945s [2026-01-30T05:48:21+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:48:22+0000] [Thread-4 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:48:22: Job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v1 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:22+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmpxnfw90z1tutorial_docker kind-apiDockerCall/instance-wj0esx48. 945s [2026-01-30T05:48:22+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v1 945s Exit reason: None 945s [2026-01-30T05:48:22+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v2 945s [2026-01-30T05:48:22+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-wj0esx48" follows: 945s =========> 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v1 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v1) from description 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v1 945s [2026-01-30T05:48:22+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v1 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:22+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:22+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:48:22+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v2 with ID kind-apiDockerCall/instance-wj0esx48 to 1 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 945s [2026-01-30T05:48:23+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmpxnfw90z1tutorial_docker kind-apiDockerCall/instance-wj0esx48. 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v3 945s Exit reason: None 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v5 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-wj0esx48" follows: 945s =========> 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4) from description 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4 945s [2026-01-30T05:48:22+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:22+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:22+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v5 with ID kind-apiDockerCall/instance-wj0esx48 to 0 945s [2026-01-30T05:48:23+0000] [MainThread] [W] [toil.leader] Job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v6 is completely failed 945s [2026-01-30T05:48:23+0000] [Thread-4 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 05:48:23: Job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:26+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.leevCg/autopkgtest_tmp/build/failed.log... 945s [2026-01-30T05:48:26+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 945s [2026-01-30T05:48:26+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v6 945s [2026-01-30T05:48:26+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.lib.history] Workflow ec00af2f-cf95-4d25-9a16-9a195ee11381 stopped. Success: False 945s [2026-01-30T05:48:27+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/tmpxnfw90z1tutorial_docker) 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py", line 20, in 945s toil.start(align) 945s ~~~~~~~~~~^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 945s return self._runMainLoop(rootJobDescription) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 945s ).run() 945s ~~~^^ 945s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 945s raise FailedJobsException( 945s ...<3 lines>... 945s ) 945s toil.exceptions.FailedJobsException: The job store '/tmp/tmpxnfw90z1tutorial_docker' contains 1 failed jobs: 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v6 945s Log from job "'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v6" follows: 945s =========> 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4 945s [2026-01-30T05:48:22+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4) from description 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4 945s [2026-01-30T05:48:22+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-wj0esx48 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:22+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:22+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_STOP - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_STOP0/working/test.txt' 945s FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_RM - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerClean_CRx_RM0/working/test.txt' 945s FAILED lib/dockerTest.py::TestDocker::testDockerPipeChain - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v6 945s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v6" follows: 945s =========> 945s [2026-01-30T05:48:39+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:39+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:39+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v4 945s [2026-01-30T05:48:40+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-md7qxf19 v4 945s [2026-01-30T05:48:40+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 945s return apiDockerCall( 945s job, 945s ...<2 lines>... 945s privileged=True, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:40+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s FAILED lib/dockerTest.py::TestDocker::testDockerPipeChainErrorDetection - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerPipeChainErrorDetect0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v6 945s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v6" follows: 945s =========> 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:45+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4 945s [2026-01-30T05:48:46+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4 945s [2026-01-30T05:48:46+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-0zhordoo v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:46+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 945s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 945s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:46+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChain - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v6 945s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v6" follows: 945s =========> 945s [2026-01-30T05:48:51+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:51+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:51+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4 945s [2026-01-30T05:48:51+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4 945s [2026-01-30T05:48:51+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-w7daaumv v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:51+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 945s return apiDockerCall( 945s job, 945s ...<2 lines>... 945s privileged=True, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:51+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChainErrorDetection - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testNonCachingDockerChainError0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v6 945s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v6" follows: 945s =========> 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4 945s [2026-01-30T05:48:56+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4 945s [2026-01-30T05:48:56+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-bb7e9btz v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:48:56+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 945s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 945s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:48:56+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s FAILED lib/dockerTest.py::TestDocker::testDockerLogs - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v6 945s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v6" follows: 945s =========> 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4 945s [2026-01-30T05:49:04+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4 945s [2026-01-30T05:49:04+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_iuhiz43 v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:04+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:04+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Stream - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v6 945s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v6" follows: 945s =========> 945s [2026-01-30T05:49:10+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:10+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:10+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4 945s [2026-01-30T05:49:11+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4 945s [2026-01-30T05:49:11+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_0gxyjha v4 used 1.03x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:11+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:11+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v6 945s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v6" follows: 945s =========> 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4 945s [2026-01-30T05:49:16+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4 945s [2026-01-30T05:49:16+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-233c3gcg v4 used 1.02x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:16+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:16+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux_Stream - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw2/testDockerLogs_Demux_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v6 945s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v6" follows: 945s =========> 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4 945s [2026-01-30T05:49:21+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4 945s [2026-01-30T05:49:21+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-dzk5e2nl v4 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 945s [2026-01-30T05:49:21+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s PermissionError: [Errno 13] Permission denied 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 945s resp = conn.urlopen( 945s method=request.method, 945s ...<9 lines>... 945s chunked=chunked, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 945s retries = retries.increment( 945s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 945s raise reraise(type(error), error, _stacktrace) 945s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 945s raise value.with_traceback(tb) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 945s response = self._make_request( 945s conn, 945s ...<10 lines>... 945s **response_kw, 945s ) 945s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 945s conn.request( 945s ~~~~~~~~~~~~^ 945s method, 945s ^^^^^^^ 945s ...<6 lines>... 945s enforce_content_length=enforce_content_length, 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 945s self.endheaders() 945s ~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 945s self._send_output(message_body, encode_chunked=encode_chunked) 945s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 945s self.send(msg) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3.13/http/client.py", line 1057, in send 945s self.connect() 945s ~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 945s sock.connect(self.unix_socket) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 945s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s During handling of the above exception, another exception occurred: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 945s return self.version(api_version=False)["ApiVersion"] 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 945s return self._result(self._get(url), json=True) 945s ~~~~~~~~~^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 945s return f(self, *args, **kwargs) 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 945s return self.get(url, **self._set_request_timeout(kwargs)) 945s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 945s return self.request("GET", url, **kwargs) 945s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 945s resp = self.send(prep, **send_kwargs) 945s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 945s r = adapter.send(request, **kwargs) 945s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 945s raise ConnectionError(err, request=request) 945s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s The above exception was the direct cause of the following exception: 945s 945s Traceback (most recent call last): 945s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 945s job._runner( 945s ~~~~~~~~~~~^ 945s jobGraph=None, 945s ^^^^^^^^^^^^^^ 945s ...<2 lines>... 945s defer=defer, 945s ^^^^^^^^^^^^ 945s ) 945s ^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 945s returnValues = self._run(jobGraph=None, fileStore=fileStore) 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 945s return self.run(fileStore) 945s ~~~~~~~~^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 945s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 945s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 945s out = apiDockerCall( 945s job, 945s ...<8 lines>... 945s demux=demux, 945s ) 945s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 945s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 945s return cls( 945s timeout=timeout, 945s ...<3 lines>... 945s **kwargs_from_env(**kwargs) 945s ) 945s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 945s self.api = APIClient(*args, **kwargs) 945s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 945s self._version = self._retrieve_server_version() 945s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 945s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 945s raise DockerException( 945s f'Error while fetching server API version: {e}' 945s ) from e 945s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 945s 945s [2026-01-30T05:49:21+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 945s <========= 945s ERROR src/importExportFileTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py'. 945s Hint: make sure your test modules/packages have valid Python names. 945s Traceback: 945s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 945s mod = import_path( 945s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 945s importlib.import_module(module_name) 945s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 945s return _bootstrap._gcd_import(name[level:], package, level) 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s :1387: in _gcd_import 945s ??? 945s :1360: in _find_and_load 945s ??? 945s :1331: in _find_and_load_unlocked 945s ??? 945s :935: in _load_unlocked 945s ??? 945s :1023: in exec_module 945s ??? 945s :488: in _call_with_frames_removed 945s ??? 945s /usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py:30: in 945s from pytest_subtests import SubTests 945s E ModuleNotFoundError: No module named 'pytest_subtests' 945s ERROR src/jobEncapsulationTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py'. 945s Hint: make sure your test modules/packages have valid Python names. 945s Traceback: 945s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 945s mod = import_path( 945s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 945s importlib.import_module(module_name) 945s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 945s return _bootstrap._gcd_import(name[level:], package, level) 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s :1387: in _gcd_import 945s ??? 945s :1360: in _find_and_load 945s ??? 945s :1331: in _find_and_load_unlocked 945s ??? 945s :935: in _load_unlocked 945s ??? 945s :1023: in exec_module 945s ??? 945s :488: in _call_with_frames_removed 945s ??? 945s /usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py:17: in 945s from toil.test.src.jobTest import fn1Test 945s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 945s from pytest_subtests import SubTests 945s E ModuleNotFoundError: No module named 'pytest_subtests' 945s ERROR src/jobTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobTest.py'. 945s Hint: make sure your test modules/packages have valid Python names. 945s Traceback: 945s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 945s mod = import_path( 945s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 945s importlib.import_module(module_name) 945s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 945s return _bootstrap._gcd_import(name[level:], package, level) 945s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 945s :1387: in _gcd_import 945s ??? 945s :1360: in _find_and_load 945s ??? 945s :1331: in _find_and_load_unlocked 945s ??? 945s :935: in _load_unlocked 945s ??? 945s :1023: in exec_module 945s ??? 945s :488: in _call_with_frames_removed 945s ??? 945s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 945s from pytest_subtests import SubTests 945s E ModuleNotFoundError: No module named 'pytest_subtests' 945s = 13 failed, 226 passed, 136 skipped, 3 errors, 24 subtests passed in 325.05s (0:05:25) = 945s E: pybuild pybuild:483: test: plugin pyproject failed with: exit code=1: cd /tmp/autopkgtest.leevCg/autopkgtest_tmp/build; python3.13 -m pytest -n 4 --dist loadscope -vv -W ignore -k "not (testVirtualEnv or DockstoreLookupTest or testMultiplejobs or testServices)" -m "not slow" --ignore /usr/lib/python3/dist-packages/toil/test/lib/aws/test_s3.py --ignore /usr/lib/python3/dist-packages/toil/test/provisioners/aws/awsProvisionerTest.py --ignore /usr/lib/python3/dist-packages/toil/test/wdl/wdltoil_test.py --ignore /usr/lib/python3/dist-packages/toil/test/cwl/cwlTest.py --ignore /usr/lib/python3/dist-packages/toil/test/lib/test_ec2.py --ignore /usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py --ignore /usr/lib/python3/dist-packages/toil/test/lib/aws/test_iam.py --ignore /usr/lib/python3/dist-packages/toil/test/provisioners/clusterTest.py --ignore /usr/lib/python3/dist-packages/toil/test/wdl/wdltoil_test_kubernetes.py --ignore /usr/lib/python3/dist-packages/toil/test/cactus/test_cactus_integration.py --pyargs toil.test 945s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.14 3.13" returned exit code 13 945s make: *** [/tmp/V2_bAwSwZH/run:4: pybuild-autopkgtest] Error 25 945s pybuild-autopkgtest: error: /tmp/V2_bAwSwZH/run pybuild-autopkgtest returned exit code 2 945s autopkgtest [05:53:41]: test pybuild-autopkgtest: -----------------------] 946s pybuild-autopkgtest FAIL non-zero exit status 25 946s autopkgtest [05:53:42]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 946s autopkgtest [05:53:42]: @@@@@@@@@@@@@@@@@@@@ summary 946s smoke-test PASS (superficial) 946s pybuild-autopkgtest FAIL non-zero exit status 25