0s autopkgtest [23:39:57]: starting date and time: 2026-01-30 23:39:57+0000 0s autopkgtest [23:39:57]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [23:39:57]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.y9ctwsj7/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-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-11.secgroup --name adt-resolute-amd64-toil-20260130-233956-juju-7f2275-prod-proposed-migration-environment-2-08cd0f94-4e9e-49b5-8775-ad368ffb1e71 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-toil-20260130-233956-juju-7f2275-prod-proposed-migration-environment-2-08cd0f94-4e9e-49b5-8775-ad368ffb1e71 from image adt/ubuntu-resolute-amd64-server-20260130.img (UUID afba56f8-6ab4-44eb-9e07-036bcbd7054f)... 73s autopkgtest [23:41:10]: testbed dpkg architecture: amd64 73s autopkgtest [23:41:10]: testbed apt version: 3.1.14 73s autopkgtest [23:41:10]: @@@@@@@@@@@@@@@@@@@@ test bed setup 73s autopkgtest [23:41:10]: testbed release detected to be: None 74s autopkgtest [23:41:11]: updating testbed package index (apt update) 74s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 74s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 74s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 74s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 74s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [4676 B] 74s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1187 kB] 74s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [26.6 kB] 74s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [105 kB] 74s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [118 kB] 74s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [101 kB] 74s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [4196 B] 74s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [6164 B] 74s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [20.9 kB] 74s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [388 B] 74s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [963 kB] 75s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [382 kB] 75s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [26.2 kB] 75s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [3336 B] 75s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [24.0 kB] 75s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [1304 B] 75s Fetched 3099 kB in 1s (4055 kB/s) 76s Reading package lists... 76s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 76s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 76s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 76s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 77s Reading package lists... 77s Reading package lists... 77s Building dependency tree... 77s Reading state information... 77s Calculating upgrade... 77s The following packages will be upgraded: 77s 3cpio bzip2 inetutils-telnet libbz2-1.0 libsqlite3-0 rng-tools-debian telnet 77s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 77s Need to get 1234 kB of archives. 77s After this operation, 18.4 kB disk space will be freed. 77s Get:1 http://ftpmaster.internal/ubuntu resolute/universe amd64 rng-tools-debian amd64 2.6build1 [46.1 kB] 77s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 bzip2 amd64 1.0.8-6build2 [34.3 kB] 77s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libbz2-1.0 amd64 1.0.8-6build2 [37.0 kB] 77s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libsqlite3-0 amd64 3.46.1-9 [722 kB] 77s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 inetutils-telnet amd64 2:2.7-2ubuntu1 [107 kB] 77s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 telnet all 0.17+2.7-2ubuntu1 [3636 B] 77s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.13.1-1ubuntu1 [284 kB] 78s dpkg-preconfigure: unable to re-open stdin: No such file or directory 78s Fetched 1234 kB in 0s (5549 kB/s) 78s (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 ... 124211 files and directories currently installed.) 78s Preparing to unpack .../rng-tools-debian_2.6build1_amd64.deb ... 78s Unpacking rng-tools-debian (2.6build1) over (2.6) ... 78s Preparing to unpack .../bzip2_1.0.8-6build2_amd64.deb ... 78s Unpacking bzip2 (1.0.8-6build2) over (1.0.8-6build1) ... 78s Preparing to unpack .../libbz2-1.0_1.0.8-6build2_amd64.deb ... 78s Unpacking libbz2-1.0:amd64 (1.0.8-6build2) over (1.0.8-6build1) ... 78s Setting up libbz2-1.0:amd64 (1.0.8-6build2) ... 78s (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 ... 124211 files and directories currently installed.) 78s Preparing to unpack .../libsqlite3-0_3.46.1-9_amd64.deb ... 78s Unpacking libsqlite3-0:amd64 (3.46.1-9) over (3.46.1-8) ... 78s Preparing to unpack .../inetutils-telnet_2%3a2.7-2ubuntu1_amd64.deb ... 78s Unpacking inetutils-telnet (2:2.7-2ubuntu1) over (2:2.6-4ubuntu1) ... 78s Preparing to unpack .../telnet_0.17+2.7-2ubuntu1_all.deb ... 78s Unpacking telnet (0.17+2.7-2ubuntu1) over (0.17+2.6-4ubuntu1) ... 78s Preparing to unpack .../3cpio_0.13.1-1ubuntu1_amd64.deb ... 78s Unpacking 3cpio (0.13.1-1ubuntu1) over (0.12.0-1ubuntu1) ... 78s Setting up 3cpio (0.13.1-1ubuntu1) ... 78s Setting up libsqlite3-0:amd64 (3.46.1-9) ... 78s Setting up inetutils-telnet (2:2.7-2ubuntu1) ... 78s Setting up bzip2 (1.0.8-6build2) ... 78s Setting up rng-tools-debian (2.6build1) ... 79s Setting up telnet (0.17+2.7-2ubuntu1) ... 79s Processing triggers for man-db (2.13.1-1) ... 79s Processing triggers for libc-bin (2.42-2ubuntu4) ... 79s autopkgtest [23:41:16]: upgrading testbed (apt dist-upgrade and autopurge) 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Calculating upgrade... 80s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Solving dependencies... 80s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s autopkgtest [23:41:17]: rebooting testbed after setup commands that affected boot 110s autopkgtest [23:41:47]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:49:02 UTC 2026 112s autopkgtest [23:41:49]: @@@@@@@@@@@@@@@@@@@@ apt-source toil 114s Get:1 http://ftpmaster.internal/ubuntu resolute/universe toil 9.1.0-1 (dsc) [2872 B] 114s Get:2 http://ftpmaster.internal/ubuntu resolute/universe toil 9.1.0-1 (tar) [7876 kB] 114s Get:3 http://ftpmaster.internal/ubuntu resolute/universe toil 9.1.0-1 (diff) [17.1 kB] 114s gpgv: Signature made Fri Oct 17 09:42:43 2025 UTC 114s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 114s gpgv: issuer "crusoe@debian.org" 114s gpgv: Can't check signature: No public key 114s dpkg-source: warning: cannot verify inline signature for ./toil_9.1.0-1.dsc: no acceptable signature found 114s autopkgtest [23:41:51]: testing package toil version 9.1.0-1 115s autopkgtest [23:41:52]: build not needed 116s autopkgtest [23:41:53]: test smoke-test: preparing testbed 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Solving dependencies... 116s The following NEW packages will be installed: 116s cwl-upgrader cwltool fontconfig fontconfig-config fonts-dejavu-core 116s fonts-dejavu-mono fonts-glyphicons-halflings graphviz libaom3 libcairo2 116s libcdt6 libcgraph8 libdatrie1 libde265-0 libdeflate0 libfontconfig1 libgd3 116s libgomp1 libgraphite2-3 libgvc7 libgvplugin-gd8 libgvplugin-pango8 libgvpr2 116s libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265 libheif1 116s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap liblerc4 116s libltdl7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 116s libpixman-1-0 libsharpyuv0 libthai-data libthai0 libtiff6 libwebp7 116s libxcb-render0 libxcb-shm0 libxdot4 libxpm4 libxrender1 libxslt1.1 116s python3-arcp python3-argcomplete python3-blessed python3-cachecontrol 116s python3-coloredlogs python3-configargparse python3-cwl-utils python3-dill 116s python3-docker python3-enlighten python3-filelock python3-humanfriendly 116s python3-lxml python3-mistune python3-msgpack python3-mypy-extensions 116s python3-networkx python3-prefixed python3-prompt-toolkit python3-prov 116s python3-psutil python3-pubsub python3-pydot python3-rdflib 116s python3-rich-argparse python3-ruamel.yaml python3-ruamel.yaml.clib 116s python3-schema-salad python3-spython python3-wcwidth toil 116s 0 upgraded, 81 newly installed, 0 to remove and 0 not upgraded. 116s Need to get 28.8 MB of archives. 116s After this operation, 167 MB of additional disk space will be used. 116s Get:1 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ruamel.yaml.clib amd64 0.2.15+ds-1 [200 kB] 116s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 python3-ruamel.yaml all 0.18.10+ds-1build1 [127 kB] 116s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-msgpack amd64 1.1.2-1 [107 kB] 116s Get:4 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cachecontrol all 0.14.3-1 [18.7 kB] 116s Get:5 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mistune all 3.1.4-1 [35.0 kB] 116s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mypy-extensions all 1.1.0-1 [6716 B] 116s Get:7 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rdflib all 7.4.0-1 [431 kB] 116s Get:8 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-filelock all 3.20.3-1 [13.5 kB] 116s Get:9 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 116s Get:10 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 116s Get:11 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-schema-salad amd64 8.9.20251102115403-1 [1843 kB] 117s Get:12 http://ftpmaster.internal/ubuntu resolute/universe amd64 cwl-upgrader all 1.2.14-1 [16.6 kB] 117s Get:13 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-argcomplete all 3.6.3-1 [36.1 kB] 117s Get:14 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-humanfriendly all 10.0-6build1 [70.9 kB] 117s Get:15 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-coloredlogs all 15.0.1-1build1 [38.4 kB] 117s Get:16 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cwl-utils all 0.40-1 [140 kB] 117s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libxslt1.1 amd64 1.1.43-0.3 [172 kB] 117s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-lxml amd64 6.0.2-1 [2333 kB] 117s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-networkx all 3.2.1-4ubuntu2 [11.8 MB] 117s Get:20 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcdt6 amd64 14.1.1-2ubuntu2 [20.1 kB] 117s Get:21 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcgraph8 amd64 14.1.1-2ubuntu2 [55.3 kB] 117s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libltdl7 amd64 2.5.4-9 [43.7 kB] 117s Get:23 http://ftpmaster.internal/ubuntu resolute/universe amd64 libpathplan4 amd64 14.1.1-2ubuntu2 [26.3 kB] 117s Get:24 http://ftpmaster.internal/ubuntu resolute/universe amd64 libxdot4 amd64 14.1.1-2ubuntu2 [23.5 kB] 117s Get:25 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgvc7 amd64 14.1.1-2ubuntu2 [397 kB] 117s Get:26 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgvpr2 amd64 14.1.1-2ubuntu2 [128 kB] 117s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 117s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB] 117s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB] 117s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB] 117s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 117s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB] 117s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B] 117s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 117s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB] 117s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB] 117s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libaom3 amd64 3.13.1-2 [1970 kB] 117s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libheif-plugin-aomdec amd64 1.21.2-1 [14.2 kB] 117s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libde265-0 amd64 1.0.16-1build1 [172 kB] 117s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libheif-plugin-libde265 amd64 1.21.2-1 [9978 B] 117s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libheif1 amd64 1.21.2-1 [544 kB] 117s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-12ubuntu1 [151 kB] 117s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 117s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 117s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 117s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 117s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB] 117s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB] 117s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB] 117s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 117s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libxpm4 amd64 1:3.5.17-1build3 [37.3 kB] 117s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libgd3 amd64 2.3.3-13ubuntu1 [130 kB] 117s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgvplugin-gd8 amd64 14.1.1-2ubuntu2 [25.5 kB] 117s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB] 117s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB] 117s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.1-1 [519 kB] 117s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB] 117s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB] 117s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB] 117s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB] 117s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB] 117s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB] 117s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgvplugin-pango8 amd64 14.1.1-2ubuntu2 [24.6 kB] 117s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 graphviz amd64 14.1.1-2ubuntu2 [58.5 kB] 117s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pydot all 4.0.1-1 [35.8 kB] 117s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-prov all 2.1.1-1 [101 kB] 117s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-psutil amd64 7.1.0-1ubuntu1 [191 kB] 117s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rich-argparse all 1.6.0-2 [17.2 kB] 117s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-spython all 0.3.13-2build1 [56.4 kB] 118s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-arcp all 0.2.1-7build1 [14.1 kB] 118s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 cwltool all 3.1.20251031082601-1 [533 kB] 118s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-wcwidth all 0.2.14+dfsg1-1build1 [26.5 kB] 118s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-blessed all 1.21.0-1 [50.4 kB] 118s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-configargparse all 1.7-2 [31.7 kB] 118s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-dill all 0.4.0-1 [84.8 kB] 118s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-docker all 7.1.0-2ubuntu1 [91.0 kB] 118s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-prefixed all 0.7.0-1build1 [8352 B] 118s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-enlighten amd64 1.11.2-1build1 [42.4 kB] 118s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-prompt-toolkit all 3.0.52-2 [258 kB] 118s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pubsub all 4.0.3-7build1 [45.0 kB] 118s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 toil all 9.1.0-1 [1104 kB] 118s Fetched 28.8 MB in 1s (20.3 MB/s) 118s Selecting previously unselected package python3-ruamel.yaml.clib. 118s (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 ... 124211 files and directories currently installed.) 118s Preparing to unpack .../00-python3-ruamel.yaml.clib_0.2.15+ds-1_amd64.deb ... 118s Unpacking python3-ruamel.yaml.clib (0.2.15+ds-1) ... 118s Selecting previously unselected package python3-ruamel.yaml. 118s Preparing to unpack .../01-python3-ruamel.yaml_0.18.10+ds-1build1_all.deb ... 118s Unpacking python3-ruamel.yaml (0.18.10+ds-1build1) ... 118s Selecting previously unselected package python3-msgpack. 118s Preparing to unpack .../02-python3-msgpack_1.1.2-1_amd64.deb ... 118s Unpacking python3-msgpack (1.1.2-1) ... 118s Selecting previously unselected package python3-cachecontrol. 118s Preparing to unpack .../03-python3-cachecontrol_0.14.3-1_all.deb ... 118s Unpacking python3-cachecontrol (0.14.3-1) ... 118s Selecting previously unselected package python3-mistune. 118s Preparing to unpack .../04-python3-mistune_3.1.4-1_all.deb ... 118s Unpacking python3-mistune (3.1.4-1) ... 118s Selecting previously unselected package python3-mypy-extensions. 118s Preparing to unpack .../05-python3-mypy-extensions_1.1.0-1_all.deb ... 118s Unpacking python3-mypy-extensions (1.1.0-1) ... 118s Selecting previously unselected package python3-rdflib. 118s Preparing to unpack .../06-python3-rdflib_7.4.0-1_all.deb ... 118s Unpacking python3-rdflib (7.4.0-1) ... 118s Selecting previously unselected package python3-filelock. 118s Preparing to unpack .../07-python3-filelock_3.20.3-1_all.deb ... 118s Unpacking python3-filelock (3.20.3-1) ... 118s Selecting previously unselected package fonts-glyphicons-halflings. 118s Preparing to unpack .../08-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 118s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 118s Selecting previously unselected package libjs-bootstrap. 118s Preparing to unpack .../09-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 118s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 118s Selecting previously unselected package python3-schema-salad. 118s Preparing to unpack .../10-python3-schema-salad_8.9.20251102115403-1_amd64.deb ... 118s Unpacking python3-schema-salad (8.9.20251102115403-1) ... 118s Selecting previously unselected package cwl-upgrader. 118s Preparing to unpack .../11-cwl-upgrader_1.2.14-1_all.deb ... 118s Unpacking cwl-upgrader (1.2.14-1) ... 118s Selecting previously unselected package python3-argcomplete. 118s Preparing to unpack .../12-python3-argcomplete_3.6.3-1_all.deb ... 118s Unpacking python3-argcomplete (3.6.3-1) ... 118s Selecting previously unselected package python3-humanfriendly. 118s Preparing to unpack .../13-python3-humanfriendly_10.0-6build1_all.deb ... 118s Unpacking python3-humanfriendly (10.0-6build1) ... 118s Selecting previously unselected package python3-coloredlogs. 118s Preparing to unpack .../14-python3-coloredlogs_15.0.1-1build1_all.deb ... 118s Unpacking python3-coloredlogs (15.0.1-1build1) ... 118s Selecting previously unselected package python3-cwl-utils. 118s Preparing to unpack .../15-python3-cwl-utils_0.40-1_all.deb ... 118s Unpacking python3-cwl-utils (0.40-1) ... 118s Selecting previously unselected package libxslt1.1:amd64. 118s Preparing to unpack .../16-libxslt1.1_1.1.43-0.3_amd64.deb ... 118s Unpacking libxslt1.1:amd64 (1.1.43-0.3) ... 119s Selecting previously unselected package python3-lxml:amd64. 119s Preparing to unpack .../17-python3-lxml_6.0.2-1_amd64.deb ... 119s Unpacking python3-lxml:amd64 (6.0.2-1) ... 119s Selecting previously unselected package python3-networkx. 119s Preparing to unpack .../18-python3-networkx_3.2.1-4ubuntu2_all.deb ... 119s Unpacking python3-networkx (3.2.1-4ubuntu2) ... 119s Selecting previously unselected package libcdt6:amd64. 119s Preparing to unpack .../19-libcdt6_14.1.1-2ubuntu2_amd64.deb ... 119s Unpacking libcdt6:amd64 (14.1.1-2ubuntu2) ... 119s Selecting previously unselected package libcgraph8:amd64. 119s Preparing to unpack .../20-libcgraph8_14.1.1-2ubuntu2_amd64.deb ... 119s Unpacking libcgraph8:amd64 (14.1.1-2ubuntu2) ... 119s Selecting previously unselected package libltdl7:amd64. 119s Preparing to unpack .../21-libltdl7_2.5.4-9_amd64.deb ... 119s Unpacking libltdl7:amd64 (2.5.4-9) ... 119s Selecting previously unselected package libpathplan4:amd64. 119s Preparing to unpack .../22-libpathplan4_14.1.1-2ubuntu2_amd64.deb ... 119s Unpacking libpathplan4:amd64 (14.1.1-2ubuntu2) ... 119s Selecting previously unselected package libxdot4:amd64. 119s Preparing to unpack .../23-libxdot4_14.1.1-2ubuntu2_amd64.deb ... 119s Unpacking libxdot4:amd64 (14.1.1-2ubuntu2) ... 119s Selecting previously unselected package libgvc7:amd64. 119s Preparing to unpack .../24-libgvc7_14.1.1-2ubuntu2_amd64.deb ... 119s Unpacking libgvc7:amd64 (14.1.1-2ubuntu2) ... 119s Selecting previously unselected package libgvpr2:amd64. 119s Preparing to unpack .../25-libgvpr2_14.1.1-2ubuntu2_amd64.deb ... 119s Unpacking libgvpr2:amd64 (14.1.1-2ubuntu2) ... 119s Selecting previously unselected package fonts-dejavu-mono. 119s Preparing to unpack .../26-fonts-dejavu-mono_2.37-8build1_all.deb ... 119s Unpacking fonts-dejavu-mono (2.37-8build1) ... 119s Selecting previously unselected package fonts-dejavu-core. 119s Preparing to unpack .../27-fonts-dejavu-core_2.37-8build1_all.deb ... 119s Unpacking fonts-dejavu-core (2.37-8build1) ... 119s Selecting previously unselected package fontconfig-config. 119s Preparing to unpack .../28-fontconfig-config_2.17.1-3ubuntu1_amd64.deb ... 119s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 119s Selecting previously unselected package libfontconfig1:amd64. 119s Preparing to unpack .../29-libfontconfig1_2.17.1-3ubuntu1_amd64.deb ... 119s Unpacking libfontconfig1:amd64 (2.17.1-3ubuntu1) ... 119s Selecting previously unselected package libpixman-1-0:amd64. 119s Preparing to unpack .../30-libpixman-1-0_0.46.4-1_amd64.deb ... 119s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 119s Selecting previously unselected package libxcb-render0:amd64. 119s Preparing to unpack .../31-libxcb-render0_1.17.0-2ubuntu1_amd64.deb ... 119s Unpacking libxcb-render0:amd64 (1.17.0-2ubuntu1) ... 119s Selecting previously unselected package libxcb-shm0:amd64. 119s Preparing to unpack .../32-libxcb-shm0_1.17.0-2ubuntu1_amd64.deb ... 119s Unpacking libxcb-shm0:amd64 (1.17.0-2ubuntu1) ... 119s Selecting previously unselected package libxrender1:amd64. 119s Preparing to unpack .../33-libxrender1_1%3a0.9.12-1_amd64.deb ... 119s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 119s Selecting previously unselected package libcairo2:amd64. 119s Preparing to unpack .../34-libcairo2_1.18.4-3_amd64.deb ... 119s Unpacking libcairo2:amd64 (1.18.4-3) ... 119s Selecting previously unselected package libsharpyuv0:amd64. 119s Preparing to unpack .../35-libsharpyuv0_1.5.0-0.1build1_amd64.deb ... 119s Unpacking libsharpyuv0:amd64 (1.5.0-0.1build1) ... 119s Selecting previously unselected package libaom3:amd64. 119s Preparing to unpack .../36-libaom3_3.13.1-2_amd64.deb ... 119s Unpacking libaom3:amd64 (3.13.1-2) ... 119s Selecting previously unselected package libheif-plugin-aomdec:amd64. 119s Preparing to unpack .../37-libheif-plugin-aomdec_1.21.2-1_amd64.deb ... 119s Unpacking libheif-plugin-aomdec:amd64 (1.21.2-1) ... 119s Selecting previously unselected package libde265-0:amd64. 119s Preparing to unpack .../38-libde265-0_1.0.16-1build1_amd64.deb ... 119s Unpacking libde265-0:amd64 (1.0.16-1build1) ... 119s Selecting previously unselected package libheif-plugin-libde265:amd64. 119s Preparing to unpack .../39-libheif-plugin-libde265_1.21.2-1_amd64.deb ... 119s Unpacking libheif-plugin-libde265:amd64 (1.21.2-1) ... 119s Selecting previously unselected package libheif1:amd64. 119s Preparing to unpack .../40-libheif1_1.21.2-1_amd64.deb ... 119s Unpacking libheif1:amd64 (1.21.2-1) ... 119s Selecting previously unselected package libgomp1:amd64. 119s Preparing to unpack .../41-libgomp1_15.2.0-12ubuntu1_amd64.deb ... 119s Unpacking libgomp1:amd64 (15.2.0-12ubuntu1) ... 119s Selecting previously unselected package libimagequant0:amd64. 119s Preparing to unpack .../42-libimagequant0_2.18.0-1build1_amd64.deb ... 119s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 119s Selecting previously unselected package libjpeg-turbo8:amd64. 119s Preparing to unpack .../43-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 119s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 119s Selecting previously unselected package libjpeg8:amd64. 119s Preparing to unpack .../44-libjpeg8_8c-2ubuntu11_amd64.deb ... 119s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 119s Selecting previously unselected package libdeflate0:amd64. 119s Preparing to unpack .../45-libdeflate0_1.23-2_amd64.deb ... 119s Unpacking libdeflate0:amd64 (1.23-2) ... 119s Selecting previously unselected package libjbig0:amd64. 119s Preparing to unpack .../46-libjbig0_2.1-6.1ubuntu3_amd64.deb ... 119s Unpacking libjbig0:amd64 (2.1-6.1ubuntu3) ... 119s Selecting previously unselected package liblerc4:amd64. 119s Preparing to unpack .../47-liblerc4_4.0.0+ds-5ubuntu2_amd64.deb ... 119s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 119s Selecting previously unselected package libwebp7:amd64. 119s Preparing to unpack .../48-libwebp7_1.5.0-0.1build1_amd64.deb ... 119s Unpacking libwebp7:amd64 (1.5.0-0.1build1) ... 119s Selecting previously unselected package libtiff6:amd64. 119s Preparing to unpack .../49-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 119s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 119s Selecting previously unselected package libxpm4:amd64. 119s Preparing to unpack .../50-libxpm4_1%3a3.5.17-1build3_amd64.deb ... 119s Unpacking libxpm4:amd64 (1:3.5.17-1build3) ... 119s Selecting previously unselected package libgd3:amd64. 119s Preparing to unpack .../51-libgd3_2.3.3-13ubuntu1_amd64.deb ... 119s Unpacking libgd3:amd64 (2.3.3-13ubuntu1) ... 119s Selecting previously unselected package libgvplugin-gd8:amd64. 119s Preparing to unpack .../52-libgvplugin-gd8_14.1.1-2ubuntu2_amd64.deb ... 119s Unpacking libgvplugin-gd8:amd64 (14.1.1-2ubuntu2) ... 119s Selecting previously unselected package fontconfig. 119s Preparing to unpack .../53-fontconfig_2.17.1-3ubuntu1_amd64.deb ... 119s Unpacking fontconfig (2.17.1-3ubuntu1) ... 119s Selecting previously unselected package libgraphite2-3:amd64. 119s Preparing to unpack .../54-libgraphite2-3_1.3.14-11ubuntu1_amd64.deb ... 119s Unpacking libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 119s Selecting previously unselected package libharfbuzz0b:amd64. 120s Preparing to unpack .../55-libharfbuzz0b_12.3.1-1_amd64.deb ... 120s Unpacking libharfbuzz0b:amd64 (12.3.1-1) ... 120s Selecting previously unselected package libthai-data. 120s Preparing to unpack .../56-libthai-data_0.1.30-1_all.deb ... 120s Unpacking libthai-data (0.1.30-1) ... 120s Selecting previously unselected package libdatrie1:amd64. 120s Preparing to unpack .../57-libdatrie1_0.2.14-1_amd64.deb ... 120s Unpacking libdatrie1:amd64 (0.2.14-1) ... 120s Selecting previously unselected package libthai0:amd64. 120s Preparing to unpack .../58-libthai0_0.1.30-1_amd64.deb ... 120s Unpacking libthai0:amd64 (0.1.30-1) ... 120s Selecting previously unselected package libpango-1.0-0:amd64. 120s Preparing to unpack .../59-libpango-1.0-0_1.57.0-1_amd64.deb ... 120s Unpacking libpango-1.0-0:amd64 (1.57.0-1) ... 120s Selecting previously unselected package libpangoft2-1.0-0:amd64. 120s Preparing to unpack .../60-libpangoft2-1.0-0_1.57.0-1_amd64.deb ... 120s Unpacking libpangoft2-1.0-0:amd64 (1.57.0-1) ... 120s Selecting previously unselected package libpangocairo-1.0-0:amd64. 120s Preparing to unpack .../61-libpangocairo-1.0-0_1.57.0-1_amd64.deb ... 120s Unpacking libpangocairo-1.0-0:amd64 (1.57.0-1) ... 120s Selecting previously unselected package libgvplugin-pango8:amd64. 120s Preparing to unpack .../62-libgvplugin-pango8_14.1.1-2ubuntu2_amd64.deb ... 120s Unpacking libgvplugin-pango8:amd64 (14.1.1-2ubuntu2) ... 120s Selecting previously unselected package graphviz. 120s Preparing to unpack .../63-graphviz_14.1.1-2ubuntu2_amd64.deb ... 120s Unpacking graphviz (14.1.1-2ubuntu2) ... 120s Selecting previously unselected package python3-pydot. 120s Preparing to unpack .../64-python3-pydot_4.0.1-1_all.deb ... 120s Unpacking python3-pydot (4.0.1-1) ... 120s Selecting previously unselected package python3-prov. 120s Preparing to unpack .../65-python3-prov_2.1.1-1_all.deb ... 120s Unpacking python3-prov (2.1.1-1) ... 120s Selecting previously unselected package python3-psutil. 120s Preparing to unpack .../66-python3-psutil_7.1.0-1ubuntu1_amd64.deb ... 120s Unpacking python3-psutil (7.1.0-1ubuntu1) ... 120s Selecting previously unselected package python3-rich-argparse. 120s Preparing to unpack .../67-python3-rich-argparse_1.6.0-2_all.deb ... 120s Unpacking python3-rich-argparse (1.6.0-2) ... 120s Selecting previously unselected package python3-spython. 120s Preparing to unpack .../68-python3-spython_0.3.13-2build1_all.deb ... 120s Unpacking python3-spython (0.3.13-2build1) ... 120s Selecting previously unselected package python3-arcp. 120s Preparing to unpack .../69-python3-arcp_0.2.1-7build1_all.deb ... 120s Unpacking python3-arcp (0.2.1-7build1) ... 120s Selecting previously unselected package cwltool. 120s Preparing to unpack .../70-cwltool_3.1.20251031082601-1_all.deb ... 120s Unpacking cwltool (3.1.20251031082601-1) ... 120s Selecting previously unselected package python3-wcwidth. 120s Preparing to unpack .../71-python3-wcwidth_0.2.14+dfsg1-1build1_all.deb ... 120s Unpacking python3-wcwidth (0.2.14+dfsg1-1build1) ... 120s Selecting previously unselected package python3-blessed. 120s Preparing to unpack .../72-python3-blessed_1.21.0-1_all.deb ... 120s Unpacking python3-blessed (1.21.0-1) ... 120s Selecting previously unselected package python3-configargparse. 120s Preparing to unpack .../73-python3-configargparse_1.7-2_all.deb ... 120s Unpacking python3-configargparse (1.7-2) ... 120s Selecting previously unselected package python3-dill. 120s Preparing to unpack .../74-python3-dill_0.4.0-1_all.deb ... 120s Unpacking python3-dill (0.4.0-1) ... 120s Selecting previously unselected package python3-docker. 120s Preparing to unpack .../75-python3-docker_7.1.0-2ubuntu1_all.deb ... 120s Unpacking python3-docker (7.1.0-2ubuntu1) ... 120s Selecting previously unselected package python3-prefixed. 120s Preparing to unpack .../76-python3-prefixed_0.7.0-1build1_all.deb ... 120s Unpacking python3-prefixed (0.7.0-1build1) ... 120s Selecting previously unselected package python3-enlighten. 120s Preparing to unpack .../77-python3-enlighten_1.11.2-1build1_amd64.deb ... 120s Unpacking python3-enlighten (1.11.2-1build1) ... 120s Selecting previously unselected package python3-prompt-toolkit. 120s Preparing to unpack .../78-python3-prompt-toolkit_3.0.52-2_all.deb ... 120s Unpacking python3-prompt-toolkit (3.0.52-2) ... 120s Selecting previously unselected package python3-pubsub. 120s Preparing to unpack .../79-python3-pubsub_4.0.3-7build1_all.deb ... 120s Unpacking python3-pubsub (4.0.3-7build1) ... 120s Selecting previously unselected package toil. 120s Preparing to unpack .../80-toil_9.1.0-1_all.deb ... 120s Unpacking toil (9.1.0-1) ... 120s Setting up libxdot4:amd64 (14.1.1-2ubuntu2) ... 120s Setting up libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 120s Setting up python3-configargparse (1.7-2) ... 120s Setting up python3-arcp (0.2.1-7build1) ... 120s Setting up libcdt6:amd64 (14.1.1-2ubuntu2) ... 120s Setting up libpixman-1-0:amd64 (0.46.4-1) ... 120s Setting up libsharpyuv0:amd64 (1.5.0-0.1build1) ... 120s Setting up libaom3:amd64 (3.13.1-2) ... 120s Setting up python3-filelock (3.20.3-1) ... 120s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 120s Setting up libxpm4:amd64 (1:3.5.17-1build3) ... 120s Setting up libxrender1:amd64 (1:0.9.12-1) ... 120s Setting up libdatrie1:amd64 (0.2.14-1) ... 120s Setting up libxcb-render0:amd64 (1.17.0-2ubuntu1) ... 120s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 120s Setting up python3-mypy-extensions (1.1.0-1) ... 120s Setting up python3-docker (7.1.0-2ubuntu1) ... 120s Setting up python3-ruamel.yaml.clib (0.2.15+ds-1) ... 120s Setting up libdeflate0:amd64 (1.23-2) ... 120s Setting up libxcb-shm0:amd64 (1.17.0-2ubuntu1) ... 120s Setting up libgomp1:amd64 (15.2.0-12ubuntu1) ... 120s Setting up python3-networkx (3.2.1-4ubuntu2) ... 121s Setting up libjbig0:amd64 (2.1-6.1ubuntu3) ... 121s Setting up python3-psutil (7.1.0-1ubuntu1) ... 121s Setting up python3-prefixed (0.7.0-1build1) ... 121s Setting up python3-wcwidth (0.2.14+dfsg1-1build1) ... 121s Setting up python3-humanfriendly (10.0-6build1) ... 121s Setting up python3-spython (0.3.13-2build1) ... 122s Setting up libpathplan4:amd64 (14.1.1-2ubuntu2) ... 122s Setting up python3-dill (0.4.0-1) ... 122s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 122s Setting up fonts-dejavu-mono (2.37-8build1) ... 122s Setting up fonts-dejavu-core (2.37-8build1) ... 122s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 122s Setting up libltdl7:amd64 (2.5.4-9) ... 122s Setting up libcgraph8:amd64 (14.1.1-2ubuntu2) ... 122s Setting up libwebp7:amd64 (1.5.0-0.1build1) ... 122s Setting up python3-ruamel.yaml (0.18.10+ds-1build1) ... 122s Setting up python3-pubsub (4.0.3-7build1) ... 122s Setting up libgvpr2:amd64 (14.1.1-2ubuntu2) ... 122s Setting up python3-rich-argparse (1.6.0-2) ... 122s Setting up python3-rdflib (7.4.0-1) ... 122s Setting up libxslt1.1:amd64 (1.1.43-0.3) ... 122s Setting up libharfbuzz0b:amd64 (12.3.1-1) ... 122s Setting up libthai-data (0.1.30-1) ... 122s Setting up python3-msgpack (1.1.2-1) ... 122s Setting up python3-cachecontrol (0.14.3-1) ... 122s Setting up libde265-0:amd64 (1.0.16-1build1) ... 122s Setting up python3-argcomplete (3.6.3-1) ... 122s Setting up python3-coloredlogs (15.0.1-1build1) ... 122s Setting up python3-mistune (3.1.4-1) ... 122s Setting up libjs-bootstrap (3.4.1+dfsg-6) ... 122s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 122s Setting up python3-prompt-toolkit (3.0.52-2) ... 123s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 123s Setting up python3-blessed (1.21.0-1) ... 123s Setting up python3-schema-salad (8.9.20251102115403-1) ... 123s Setting up libthai0:amd64 (0.1.30-1) ... 123s Setting up python3-enlighten (1.11.2-1build1) ... 123s Setting up cwl-upgrader (1.2.14-1) ... 123s Setting up libgvc7:amd64 (14.1.1-2ubuntu2) ... 123s Setting up python3-lxml:amd64 (6.0.2-1) ... 123s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 123s Setting up libfontconfig1:amd64 (2.17.1-3ubuntu1) ... 123s Setting up fontconfig (2.17.1-3ubuntu1) ... 125s Regenerating fonts cache... done. 125s Setting up libpango-1.0-0:amd64 (1.57.0-1) ... 125s Setting up python3-cwl-utils (0.40-1) ... 126s Setting up libcairo2:amd64 (1.18.4-3) ... 126s Setting up libpangoft2-1.0-0:amd64 (1.57.0-1) ... 126s Setting up libpangocairo-1.0-0:amd64 (1.57.0-1) ... 126s Setting up libgvplugin-pango8:amd64 (14.1.1-2ubuntu2) ... 126s Setting up libheif-plugin-aomdec:amd64 (1.21.2-1) ... 126s Setting up libheif-plugin-libde265:amd64 (1.21.2-1) ... 126s Setting up libheif1:amd64 (1.21.2-1) ... 126s Setting up libgd3:amd64 (2.3.3-13ubuntu1) ... 126s Setting up libgvplugin-gd8:amd64 (14.1.1-2ubuntu2) ... 126s Setting up graphviz (14.1.1-2ubuntu2) ... 126s Setting up python3-pydot (4.0.1-1) ... 126s Setting up python3-prov (2.1.1-1) ... 126s Setting up cwltool (3.1.20251031082601-1) ... 127s Setting up toil (9.1.0-1) ... 127s Processing triggers for libc-bin (2.42-2ubuntu4) ... 127s Processing triggers for man-db (2.13.1-1) ... 128s autopkgtest [23:42:05]: test smoke-test: [----------------------- 129s Usage: toil COMMAND ... 129s toil --help 129s toil COMMAND --help 129s 129s Where COMMAND is one of the following: 129s 129s clean - Delete a job store used by a previous Toil workflow invocation. 129s config - Create a config file with all default Toil options. 129s debug-file - Debug tool for copying files contained in a toil jobStore. 129s debug-job - Debug tool for running a toil job locally. 129s destroy-cluster - Terminates the specified cluster and associated resources. 129s kill - Kills rogue toil processes. 129s launch-cluster - Launches a toil leader instance with the specified provisioner. 129s rsync-cluster - Rsyncs into the toil appliance container running on the leader of the cluster. 129s server - CLI entry for the Toil servers. 129s ssh-cluster - SSH into the toil appliance container running on the leader of the cluster. 129s stats - Reports statistical data about a given Toil workflow. 129s status - Tool for reporting on job status. 129s 129s 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: 129s 129s pip install cwltool==3.1.20250110105449 129s 129s usage: toil-cwl-runner [options] WORKFLOW [INFILE] [WF_OPTIONS...] 129s 129s positional arguments: 129s 129s WORKFLOW CWL file to run. 129s 129s INFILE YAML or JSON file of workflow inputs. 129s 129s WF_OPTIONS Additional inputs to the workflow as command-line 129s flags. If CWL workflow takes an input, the name of the 129s input can be used as an option. For example: 129s 129s toil-cwl-runner workflow.cwl --file1 file 129s 129s If an input has the same name as a Toil option, pass 129s '--' before it. 129s 129s options: 129s -h, --help show this help message and exit 129s --not-strict 129s --enable-dev Enable loading and running development versions of CWL 129s --enable-ext Enable loading and running 'cwltool:' extensions to 129s the CWL standards. 129s --quiet 129s --basedir BASEDIR 129s --outdir OUTDIR 129s --version show program's version number and exit 129s --log-dir LOG_DIR Log your tools stdout/stderr to this location outside 129s of container 129s --user-space-docker-cmd USER_SPACE_DOCKER_CMD 129s (Linux/OS X only) Specify a user space docker command 129s (like udocker or dx-docker) that will be used to call 129s 'pull' and 'run' 129s --singularity Use Singularity runtime for running containers. 129s Requires Singularity v2.6.1+ and Linux with kernel 129s version v3.18+ or with overlayfs support backported. 129s --podman Use Podman runtime for running containers. 129s --no-container Do not execute jobs in a Docker container, even when 129s `DockerRequirement` is specified under `hints`. 129s --leave-container Do not delete Docker container used by jobs after they 129s exit 129s --custom-net CUSTOM_NET 129s Specify docker network name to pass to docker run 129s command 129s --no-prepull Do not prepull the container prior to running the 129s workflow 129s --preserve-environment VAR1 VAR2 [VAR1 VAR2 ...] 129s Preserve specified environment variables when running 129s CommandLineTools 129s --preserve-entire-environment 129s Preserve all environment variable when running 129s CommandLineTools. 129s --beta-dependency-resolvers-configuration BETA_DEPENDENCY_RESOLVERS_CONFIGURATION 129s --beta-dependencies-directory BETA_DEPENDENCIES_DIRECTORY 129s --beta-use-biocontainers 129s --beta-conda-dependencies 129s --tmpdir-prefix TMPDIR_PREFIX 129s Path prefix for temporary directories 129s --tmp-outdir-prefix TMP_OUTDIR_PREFIX 129s Path prefix for intermediate output directories 129s --force-docker-pull Pull latest docker image even if it is locally present 129s --no-match-user Disable passing the current uid to `docker run --user` 129s --no-read-only Do not set root directory in the container as read- 129s only 129s --strict-memory-limit 129s When running with software containers and the Docker 129s engine, pass either the calculated memory allocation 129s from ResourceRequirements or the default of 1 gigabyte 129s to Docker's --memory option. 129s --strict-cpu-limit When running with software containers and the Docker 129s engine, pass either the calculated cpu allocation from 129s ResourceRequirements or the default of 1 core to 129s Docker's --cpu option. Requires docker version >= 129s v1.13. 129s --relax-path-checks Relax requirements on path names to permit spaces and 129s hash characters. 129s --default-container DEFAULT_CONTAINER 129s Specify a default docker container that will be used 129s if the workflow fails to specify one. 129s --compute-checksum Compute checksum of contents while collecting outputs 129s --no-compute-checksum 129s Do not compute checksum of contents while collecting 129s outputs 129s --eval-timeout EVAL_TIMEOUT 129s Time to wait for a Javascript expression to evaluate 129s before giving an error, default 20s. 129s --overrides OVERRIDES 129s Read process requirement overrides from file. 129s --mpi-config-file MPI_CONFIG_FILE 129s Platform specific configuration for MPI (parallel 129s launcher, its flag etc). See the cwltool README 129s section 'Running MPI-based tools' for details of the 129s format: https://github.com/common-workflow- 129s language/cwltool#running-mpi-based-tools-that-need-to- 129s be-launched 129s --bypass-file-store Do not use Toil's file store and assume all paths are 129s accessible in place from all nodes. 129s --reference-inputs Do not copy remote inputs into Toil's file store and 129s assume they are accessible in place from all nodes. 129s --disable-streaming Disable file streaming for files that have 129s 'streamable' flag True. 129s --cwl-default-ram Apply CWL specification default ramMin. 129s --no-cwl-default-ram Do not apply CWL specification default ramMin, so that 129s Toil --defaultMemory applies. This can help jobs get 129s to Slurm with no memory limit assigned. 129s --cwl-min-ram CWL_MIN_RAM 129s Specify a minimum memory allocation for all tasks .If 129s --no-cwl-default-ram is passed, this does not apply to 129s tools that do not specify a memory requirement; 129s --defaultMemory is used for those toolsin that case. 129s --destBucket DESTBUCKET 129s Specify a cloud bucket endpoint for output files. 129s --cachedir CACHEDIR Directory to cache intermediate workflow outputs to 129s avoid recomputing steps. Can be very helpful in the 129s development and troubleshooting of CWL documents. This 129s automatically bypasses the file store. Not to be 129s confused with --caching. 129s --runImportsOnWorkers, --run-imports-on-workers 129s Run the file imports on a worker instead of the 129s leader. This is useful if the leader is not optimized 129s for high network performance. If set to true, the 129s argument --importWorkersDisk must also be set. 129s --importWorkersBatchSize, --import-workers-batch-size IMPORT_WORKERS_BATCHSIZE 129s Specify the target total file size for file import 129s batches. As many files as can fit will go into each 129s batch import job. This should be set in conjunction 129s with the argument --runImportsOnWorkers. 129s --importWorkersDisk, --import-workers-disk IMPORT_WORKERS_DISK 129s Specify the disk size each import worker will get. 129s This usually will not need to be set as Toil will 129s attempt to use file streaming when downloading files. 129s If not possible, for example, when downloading from 129s AWS to a GCE job store, this should be set to the 129s largest file size of all files to import. This should 129s be set in conjunction with the arguments 129s --runImportsOnWorkers and --importWorkersBatchSize. 129s 129s --config PATH Get options from a config file. 129s 129s Logging Options: 129s --logCritical Set logging level to Critical. Default: INFO. 129s --logError Set logging level to Error. Default: INFO. 129s --logWarning Set logging level to Warning. Default: INFO. 129s --logInfo Set logging level to Info. Default: INFO. 129s --logDebug Set logging level to Debug. Default: INFO. 129s --logTrace Set logging level to Trace. Default: INFO. 129s --logOff Same as --logCritical. 129s --logLevel {Critical,Error,Warning,Info,Debug,Trace,critical,error,warning,info,debug,trace,CRITICAL,ERROR,WARNING,INFO,DEBUG,TRACE} 129s Set the log level. Default: INFO. Options: 129s ['Critical', 'Error', 'Warning', 'Info', 'Debug', 129s 'Trace', 'critical', 'error', 'warning', 'info', 129s 'debug', 'trace', 'CRITICAL', 'ERROR', 'WARNING', 129s 'INFO', 'DEBUG', 'TRACE']. 129s --logFile LOGFILE File to log in. 129s --rotatingLogging Turn on rotating logging, which prevents log files 129s from getting too big. 129s --logColors BOOL Enable or disable colored logging. Default: True 129s 129s Toil core options: 129s Options to specify the location of the Toil workflow and turn on stats collation about the performance of jobs. 129s 129s --jobstore, --jobStore JOBSTORE 129s The location of the job store for the workflow. A job 129s store holds persistent information about the jobs, 129s stats, and files in a workflow. If the workflow is run 129s with a distributed batch system, the job store must be 129s accessible by all worker nodes. Depending on the 129s desired job store implementation, the location should 129s be formatted according to one of the following 129s schemes: file: where points to a 129s directory on the file system aws:: 129s where is the name of an AWS region like us- 129s west-2 and will be prepended to the names of 129s any top-level AWS resources in use by job store, e.g. 129s S3 buckets. google:: TODO: explain 129s For backwards compatibility, you may also specify 129s ./foo (equivalent to file:./foo or just file:foo) or 129s /bar (equivalent to file:/bar). 129s --workDir PATH Absolute path to directory where temporary files 129s generated during the Toil run should be placed. 129s Standard output and error from batch system jobs 129s (unless --noStdOutErr is set) will be placed in this 129s directory. A cache directory may be placed in this 129s directory. Temp files and folders will be placed in a 129s directory toil- within workDir. The 129s workflowID is generated by Toil and will be reported 129s in the workflow logs. Default is determined by the 129s variables (TMPDIR, TEMP, TMP) via mkdtemp. This 129s directory needs to exist on all machines running jobs; 129s if capturing standard output and error from batch 129s system jobs is desired, it will generally need to be 129s on a shared file system. When sharing a cache between 129s containers on a host, this directory must be shared 129s between the containers. [env var: TOIL_WORKDIR] 129s --coordinationDir PATH 129s Absolute path to directory where Toil will keep state 129s and lock files. When sharing a cache between 129s containers on a host, this directory must be shared 129s between the containers. [env var: 129s TOIL_COORDINATION_DIR] 129s --noStdOutErr Do not capture standard output and error from batch 129s system jobs. 129s --stats Keep statistics about the toil workflow to be used by 129s 'toil stats'. 129s --clean {always,onError,never,onSuccess} 129s Determines the deletion of the jobStore upon 129s completion of the program. Choices: ['always', 129s 'onError', 'never', 'onSuccess']. The --stats option 129s requires information from the jobStore upon completion 129s so the jobStore will never be deleted with that flag. 129s If you wish to be able to restart the run, choose 129s 'never' or 'onSuccess'. Default is 'never' if stats is 129s enabled, and 'onSuccess' otherwise. 129s --cleanWorkDir {always,onError,never,onSuccess} 129s Determines deletion of temporary worker directory upon 129s completion of a job. Choices: ['always', 'onError', 129s 'never', 'onSuccess']. Default = always. WARNING: This 129s option should be changed for debugging only. Running a 129s full pipeline with this option could fill your disk 129s with excessive intermediate data. 129s --clusterStats [OPT_PATH] 129s If enabled, writes out JSON resource usage statistics 129s to a file. The default location for this file is the 129s current working directory, but an absolute path can 129s also be passed to specify where this file should be 129s written. This options only applies when using scalable 129s batch systems. 129s 129s Toil options for restarting an existing workflow: 129s Allows the restart of an existing workflow 129s 129s --restart If --restart is specified then will attempt to restart 129s existing workflow at the location pointed to by the 129s --jobStore option. Will raise an exception if the 129s workflow does not exist 129s 129s Toil options for specifying the batch system: 129s Allows the specification of the batch system. 129s 129s --batchSystem {aws_batch,single_machine,grid_engine,lsf,mesos,slurm,torque,htcondor,kubernetes} 129s The type of batch system to run the job(s) with, 129s currently can be one of aws_batch, single_machine, 129s grid_engine, lsf, mesos, slurm, torque, htcondor, 129s kubernetes. Default = single_machine 129s --disableHotDeployment 129s Hot-deployment was renamed to auto-deployment. Option 129s now redirects to --disableAutoDeployment. Left in for 129s backwards compatibility. 129s --disableAutoDeployment DISABLEAUTODEPLOYMENT 129s Should auto-deployment of Toil Python workflows be 129s deactivated? If True, the workflow's Python code 129s should be present at the same location on all workers. 129s Default = False. 129s --maxJobs MAX_JOBS Specifies the maximum number of jobs to submit to the 129s backing scheduler at once. Not supported on Mesos or 129s AWS Batch. Use 0 for unlimited. Defaults to unlimited. 129s --maxLocalJobs MAX_LOCAL_JOBS 129s Specifies the maximum number of housekeeping jobs to 129s run sumultaneously on the local system. Use 0 for 129s unlimited. Defaults to the number of local cores (4). 129s --manualMemArgs Do not add the default arguments: 'hv=MEMORY' & 129s 'h_vmem=MEMORY' to the qsub call, and instead rely on 129s TOIL_GRIDGENGINE_ARGS to supply alternative arguments. 129s Requires that TOIL_GRIDGENGINE_ARGS be set. 129s --runLocalJobsOnWorkers, --runCwlInternalJobsOnWorkers 129s Whether to run jobs marked as local (e.g. CWLScatter) 129s on the worker nodes instead of the leader node. If 129s false (default), then all such jobs are run on the 129s leader node. Setting this to true can speed up CWL 129s pipelines for very large workflows with many sub- 129s workflows and/or scatters, provided that the worker 129s pool is large enough. 129s --coalesceStatusCalls 129s Ask for job statuses from the batch system in a batch. 129s Deprecated; now always enabled where supported. 129s --statePollingWait STATEPOLLINGWAIT 129s Time, in seconds, to wait before doing a scheduler 129s query for job state. Return cached results if within 129s the waiting period. Only works for grid engine batch 129s systems such as gridengine, htcondor, torque, slurm, 129s and lsf. 129s --statePollingTimeout STATE_POLLING_TIMEOUT 129s Time, in seconds, to retry against a broken scheduler. 129s Only works for grid engine batch systems such as 129s gridengine, htcondor, torque, slurm, and lsf. 129s --batchLogsDir BATCH_LOGS_DIR 129s Directory to tell the backing batch system to log 129s into. Should be available on both the leader and the 129s workers, if the backing batch system writes logs to 129s the worker machines' filesystems, as many HPC 129s schedulers do. If unset, the Toil work directory will 129s be used. Only works for grid engine batch systems such 129s as gridengine, htcondor, torque, slurm, and lsf. [env 129s var: TOIL_BATCH_LOGS_DIR] 129s --memoryIsProduct If the batch system understands requested memory as a 129s product of the requested memory and the numberof 129s cores, set this flag to properly allocate memory. 129s --awsBatchRegion AWS_BATCH_REGION 129s The AWS region containing the AWS Batch queue to 129s submit to. [env var: TOIL_AWS_REGION] 129s --awsBatchQueue AWS_BATCH_QUEUE 129s The name or ARN of the AWS Batch queue to submit to. 129s [env var: TOIL_AWS_BATCH_QUEUE] 129s --awsBatchJobRoleArn AWS_BATCH_JOB_ROLE_ARN 129s The ARN of an IAM role to run AWS Batch jobs as, so 129s they can e.g. access a job store. Must be assumable by 129s ecs-tasks.amazonaws.com. [env var: 129s TOIL_AWS_BATCH_JOB_ROLE_ARN] 129s --scale SCALE A scaling factor to change the value of all submitted 129s tasks's submitted cores. Used in the single_machine 129s batch system. Useful for running workflows on smaller 129s machines than they were designed for, by setting a 129s value less than 1. (default: 1) 129s --slurmAllocateMem SLURM_ALLOCATE_MEM 129s If False, do not use --mem. Used as a workaround for 129s Slurm clusters that reject jobs with memory 129s allocations. [env var: TOIL_SLURM_ALLOCATE_MEM] 129s --slurmDefaultAllMem SLURM_DEFAULT_ALL_MEM 129s If True, assign Toil jobs without their own memory 129s requirements all available memory on a Slurm node (via 129s Slurm --mem=0). [env var: TOIL_SLURM_DEFAULT_ALL_MEM] 129s --slurmTime SLURM_TIME 129s Slurm job time limit, in [DD-]HH:MM:SS format. [env 129s var: TOIL_SLURM_TIME] 129s --slurmPartition SLURM_PARTITION 129s Partition to send Slurm jobs to. [env var: 129s TOIL_SLURM_PARTITION] 129s --slurmGPUPartition SLURM_GPU_PARTITION 129s Partition to send Slurm jobs to if they ask for GPUs. 129s [env var: TOIL_SLURM_GPU_PARTITION] 129s --slurmPE SLURM_PE Special partition to send Slurm jobs to if they ask 129s for more than 1 CPU. [env var: TOIL_SLURM_PE] 129s --slurmArgs SLURM_ARGS 129s Extra arguments to pass to Slurm. [env var: 129s TOIL_SLURM_ARGS] 129s 129s Toil options for configuring storage: 129s Allows configuring Toil's data storage. 129s 129s --symlinkImports BOOL 129s When using a filesystem based job store, CWL input 129s files are by default symlinked in. Setting this option 129s to True instead copies the files into the job store, 129s which may protect them from being modified externally. 129s When set to False, as long as caching is enabled, Toil 129s will protect the file automatically by changing the 129s permissions to read-only. default=True 129s --moveOutputs BOOL When using a filesystem based job store, output files 129s are by default moved to the output directory, and a 129s symlink to the moved exported file is created at the 129s initial location. Setting this option to True instead 129s copies the files into the output directory. Applies to 129s filesystem-based job stores only. default=False 129s --caching BOOL Enable or disable worker level file caching for your 129s workflow, specifying this overrides default from batch 129s system. Does not affect CWL or WDL task caching. 129s --symlinkJobStoreReads BOOL 129s Allow reads and container mounts from a JobStore's 129s shared filesystem directly via symlink. default=True 129s 129s Toil options for autoscaling the cluster of worker nodes: 129s 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. 129s 129s --provisioner, -p {aws,gce,None} 129s The provisioner for cluster auto-scaling. This is the 129s main Toil '--provisioner' option, and defaults to None 129s for running on single machine and non-auto-scaling 129s batch systems. The currently supported choices are 129s ['aws', 'gce', None]. The default is None. 129s --nodeTypes NODETYPES 129s Specifies a list of comma-separated node types, each 129s of which is composed of slash-separated instance 129s types, and an optional spot bid set off by a colon, 129s making the node type preemptible. Instance types may 129s appear in multiple node types, and the same node type 129s may appear as both preemptible and non-preemptible. 129s Valid argument specifying two node types: 129s c5.4xlarge/c5a.4xlarge:0.42,t2.large Node types: 129s c5.4xlarge/c5a.4xlarge:0.42 and t2.large Instance 129s types: c5.4xlarge, c5a.4xlarge, and t2.large 129s Semantics: Bid $0.42/hour for either c5.4xlarge or 129s c5a.4xlarge instances, treated interchangeably, while 129s they are available at that price, and buy t2.large 129s instances at full price. default=[] 129s --maxNodes INT[,INT...] 129s Maximum number of nodes of each type in the cluster, 129s if using autoscaling, provided as a comma-separated 129s list. The first value is used as a default if the list 129s length is less than the number of nodeTypes. 129s default=[10] 129s --minNodes INT[,INT...] 129s Mininum number of nodes of each type in the cluster, 129s if using auto-scaling. This should be provided as a 129s comma-separated list of the same length as the list of 129s node types. default=[0] 129s --targetTime INT Sets how rapidly you aim to complete jobs in seconds. 129s Shorter times mean more aggressive parallelization. 129s The autoscaler attempts to scale up/down so that it 129s expects all queued jobs will complete within 129s targetTime seconds. default=1800 129s --betaInertia FLOAT A smoothing parameter to prevent unnecessary 129s oscillations in the number of provisioned nodes. This 129s controls an exponentially weighted moving average of 129s the estimated number of nodes. A value of 0.0 disables 129s any smoothing, and a value of 0.9 will smooth so much 129s that few changes will ever be made. Must be between 129s 0.0 and 0.9. default=0.1 129s --scaleInterval INT The interval (seconds) between assessing if the scale 129s of the cluster needs to change. default=60 129s --preemptibleCompensation, --preemptableCompensation FLOAT 129s The preference of the autoscaler to replace 129s preemptible nodes with non-preemptible nodes, when 129s preemptible nodes cannot be started for some reason. 129s This value must be between 0.0 and 1.0, inclusive. A 129s value of 0.0 disables such compensation, a value of 129s 0.5 compensates two missing preemptible nodes with a 129s non-preemptible one. A value of 1.0 replaces every 129s missing pre-emptable node with a non-preemptible one. 129s default=0.0 129s --nodeStorage INT Specify the size of the root volume of worker nodes 129s when they are launched in gigabytes. You may want to 129s set this if your jobs require a lot of disk space. 129s (default=50). 129s --nodeStorageOverrides NODETYPE:NODESTORAGE[,NODETYPE:NODESTORAGE...] 129s Comma-separated list of nodeType:nodeStorage that are 129s used to override the default value from --nodeStorage 129s for the specified nodeType(s). This is useful for 129s heterogeneous jobs where some tasks require much more 129s disk than others. 129s --metrics BOOL Enable the prometheus/grafana dashboard for monitoring 129s CPU/RAM usage, queue size, and issued jobs. 129s --assumeZeroOverhead BOOL 129s Ignore scheduler and OS overhead and assume jobs can 129s use every last byte of memory and disk on a node when 129s autoscaling. 129s 129s Toil options for cores/memory requirements: 129s 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. 129s 129s --defaultMemory DEFAULTMEMORY 129s The default amount of memory to request for a job. 129s Only applicable to jobs that do not specify an 129s explicit value for this requirement. Standard suffixes 129s like K, Ki, M, Mi, G or Gi are supported. Default is 129s 2.0 Gi. 129s --defaultCores FLOAT The default amount of cpu to request for a job. Only 129s applicable to jobs that do not specify an explicit 129s value for this requirement. Fractions of a core (for 129s example 0.1) are supported on some batch systems 129s [mesos, single_machine]. Default is 1. 129s --defaultDisk INT The default amount of disk to request for a job. Only 129s applicable to jobs that do not specify an explicit 129s value for this requirement. Standard suffixes like K, 129s Ki, M, Mi, G or Gi are supported. Default is 2.0 Gi. 129s --defaultAccelerators ACCELERATOR[,ACCELERATOR...] 129s The default amount of accelerators to request for a 129s job. Only applicable to jobs that do not specify an 129s explicit value for this requirement. Each accelerator 129s specification can have a type (gpu [default], nvidia, 129s amd, cuda, rocm, opencl, or a specific model like 129s nvidia-tesla-k80), and a count [default: 1]. If both a 129s type and a count are used, they must be separated by a 129s colon. If multiple types of accelerators are used, the 129s specifications are separated by commas. Default is []. 129s --defaultPreemptible, --defaultPreemptable [BOOL] 129s Make all jobs able to run on preemptible (spot) nodes 129s by default. 129s --maxCores INT The max amount of cpu to request for a job. Only 129s applicable to jobs that do not specify an explicit 129s value for this requirement. Fractions of a core (for 129s example 0.1) are supported on some batch systems 129s [mesos, single_machine]. Default is 129s 9223372036854775807. 129s --maxMemory INT The max amount of memory to request for a job. Only 129s applicable to jobs that do not specify an explicit 129s value for this requirement. Standard suffixes like K, 129s Ki, M, Mi, G or Gi are supported. Default is 8.0 Ei. 129s --maxDisk INT The max amount of disk to request for a job. Only 129s applicable to jobs that do not specify an explicit 129s value for this requirement. Standard suffixes like K, 129s Ki, M, Mi, G or Gi are supported. Default is 8.0 Ei. 129s 129s Toil options for rescuing/killing/restarting jobs: 129s The options for jobs that either run too long/fail or get lost (some batch systems have issues!). 129s 129s --retryCount INT Number of times to retry a failing job before giving 129s up and labeling job failed. default=1 129s --stopOnFirstFailure BOOL 129s Stop the workflow at the first complete job failure. 129s --enableUnlimitedPreemptibleRetries, --enableUnlimitedPreemptableRetries BOOL 129s If set, preemptible failures (or any failure due to an 129s instance getting unexpectedly terminated) will not 129s count towards job failures and --retryCount. 129s --doubleMem BOOL If set, batch jobs which die to reaching memory limit 129s on batch schedulers will have their memory doubled and 129s they will be retried. The remaining retry count will 129s be reduced by 1. Currently supported by LSF. 129s --maxJobDuration INT Maximum runtime of a job (in seconds) before we kill 129s it (this is a lower bound, and the actual time before 129s killing the job may be longer). 129s default=9223372036854775807 129s --rescueJobsFrequency INT 129s Period of time to wait (in seconds) between checking 129s for missing/overlong jobs, that is jobs which get lost 129s by the batch system. Expert parameter. default=60 129s --jobStoreTimeout FLOAT 129s Maximum time (in seconds) to wait for a job's update 129s to the job store before declaring it failed. 129s default=30 129s 129s Toil log management options: 129s Options for how Toil should manage its logs. 129s 129s --maxLogFileSize MAXLOGFILESIZE 129s The maximum size of a job log file to keep (in bytes), 129s log files larger than this will be truncated to the 129s last X bytes. Setting this option to zero will prevent 129s any truncation. Setting this option to a negative 129s value will truncate from the beginning. Default=100.0 129s Mi 129s --writeLogs [OPT_PATH] 129s Write worker logs received by the leader into their 129s own files at the specified path. Any non-empty 129s standard output and error from failed batch system 129s jobs will also be written into files at this path. The 129s current working directory will be used if a path is 129s not specified explicitly. Note: By default only the 129s logs of failed jobs are returned to leader. Set log 129s level to 'debug' or enable '--writeLogsFromAllJobs' to 129s get logs back from successful jobs, and adjust 129s 'maxLogFileSize' to control the truncation limit for 129s worker logs. 129s --writeLogsGzip [OPT_PATH] 129s Identical to --writeLogs except the logs files are 129s gzipped on the leader. 129s --writeLogsFromAllJobs BOOL 129s Whether to write logs from all jobs (including the 129s successful ones) without necessarily setting the log 129s level to 'debug'. Ensure that either --writeLogs or 129s --writeLogsGzip is set if enabling this option. 129s --writeMessages PATH File to send messages from the leader's message bus 129s to. 129s --realTimeLogging BOOL 129s Enable real-time logging from workers to leader 129s 129s Toil miscellaneous options: 129s Everything else. 129s 129s --disableChaining BOOL 129s Disables chaining of jobs (chaining uses one job's 129s resource allocation for its successor job if 129s possible). 129s --disableJobStoreChecksumVerification BOOL 129s Disables checksum verification for files transferred 129s to/from the job store. Checksum verification is a 129s safety check to ensure the data is not corrupted 129s during transfer. Currently only supported for non- 129s streaming AWS files. 129s --sseKey PATH Path to file containing 32 character key to be used 129s for server-side encryption on awsJobStore or 129s googleJobStore. SSE will not be used if this flag is 129s not passed. 129s --setEnv, -e NAME=VALUE or NAME 129s Set an environment variable early on in the worker. If 129s VALUE is null, it will be looked up in the current 129s environment. Independently of this option, the worker 129s will try to emulate the leader's environment before 129s running a job, except for some variables known to vary 129s across systems. Using this option, a variable can be 129s injected into the worker process itself before it is 129s started. 129s --servicePollingInterval FLOAT 129s Interval of time service jobs wait between polling for 129s the existence of the keep-alive flag. Default: 60.0 129s --forceDockerAppliance BOOL 129s Disables sanity checking the existence of the docker 129s image specified by TOIL_APPLIANCE_SELF, which Toil 129s uses to provision mesos for autoscaling. 129s --statusWait INT Seconds to wait between reports of running jobs. 129s --disableProgress Disables the progress bar shown when standard error is 129s a terminal. 129s --publishWorkflowMetrics {all,current,no} 129s Whether to publish workflow metrics reports (including 129s unique workflow and task run IDs, job names, and 129s version and Toil feature use information) to Dockstore 129s when a workflow completes. Selecting "current" will 129s publish metrics for the current workflow. Selecting 129s "all" will also publish prior workflow runs from the 129s Toil history database, even if they themselves were 129s run with "no". Note that once published, workflow 129s metrics CANNOT be deleted or un-published; they will 129s stay published forever! 129s 129s Toil debug options: 129s Debug options for finding problems or helping with testing. 129s 129s --debugWorker Experimental no forking mode for local debugging. 129s Specifically, workers are not forked and stderr/stdout 129s are not redirected to the log. 129s --disableWorkerOutputCapture 129s Let worker output go to worker's standard out/error 129s instead of per-job logs. 129s --badWorker FLOAT For testing purposes randomly kill --badWorker 129s proportion of jobs using SIGKILL. default=0.0 129s --badWorkerFailInterval FLOAT 129s When killing the job pick uniformly within the 129s interval from 0.0 to --badWorkerFailInterval seconds 129s after the worker starts. default=0.01 129s 129s Options for recording the Docker container identifier into a file.: 129s --cidfile-dir CIDFILE_DIR 129s Store the Docker container ID into a file in the 129s specified directory. 129s --cidfile-prefix CIDFILE_PREFIX 129s Specify a prefix to the container ID filename. Final 129s file name will be followed by a timestamp. The default 129s is no prefix. 129s 129s Options for recording provenance information of the execution: 129s --provenance PROVENANCE 129s Save provenance to specified folder as a Research 129s Object that captures and aggregates workflow execution 129s and data products. 129s --enable-user-provenance 129s Record user account info as part of provenance. 129s --disable-user-provenance 129s Do not record user account info in provenance. 129s --enable-host-provenance 129s Record host info as part of provenance. 129s --disable-host-provenance 129s Do not record host info in provenance. 129s --orcid ORCID Record user ORCID identifier as part of provenance, 129s e.g. https://orcid.org/0000-0002-1825-0097 or 129s 0000-0002-1825-0097. Alternatively the environment 129s variable ORCID may be set. 129s --full-name CWL_FULL_NAME 129s Record full name of user as part of provenance, e.g. 129s Josiah Carberry. You may need to use shell quotes to 129s preserve spaces. Alternatively the environment 129s variable CWL_FULL_NAME may be set. 129s 129s Args that start with '--' can also be set in a config file 129s (/home/ubuntu/.toil/default.yaml or specified via --config). The config file 129s uses YAML syntax and must represent a YAML 'mapping' (for details, see 129s http://learn.getgrav.org/advanced/yaml). In general, command-line values 129s override environment variables which override config file values which 129s override defaults. 130s autopkgtest [23:42:07]: test smoke-test: -----------------------] 130s smoke-test PASS (superficial) 130s autopkgtest [23:42:07]: test smoke-test: - - - - - - - - - - results - - - - - - - - - - 130s autopkgtest [23:42:07]: test pybuild-autopkgtest: preparing testbed 130s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s Solving dependencies... 131s The following NEW packages will be installed: 131s autoconf automake autopoint autotools-dev build-essential containerd cpp 131s cpp-15 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu cwl-utils cwltest 131s cwltool-doc debhelper debugedit dh-autoreconf dh-python 131s dh-strip-nondeterminism docker.io docutils-common dwz fonts-font-awesome 131s fonts-lato g++ g++-15 g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 131s gcc-15 gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian 131s libarchive-zip-perl libasan8 libcc1-0 libdebhelper-perl 131s libfile-stripnondeterminism-perl libgcc-15-dev libhwasan0 libisl23 libitm1 131s libjs-jquery libjs-underscore libjson-perl liblsan0 libmpc3 131s libpython3.14-minimal libpython3.14-stdlib libquadmath0 libstdc++-15-dev 131s libtool libtsan2 libubsan1 m4 po-debconf pybuild-plugin-autopkgtest 131s pybuild-plugin-pyproject python3-alabaster python3-all python3-antlr4 131s python3-astroid python3-build python3-defusedxml python3-doc 131s python3-docutils python3-execnet python3-imagesize python3-iniconfig 131s python3-installer python3-junit.xml python3-pluggy python3-pyproject-hooks 131s python3-pytest python3-pytest-httpserver python3-pytest-timeout 131s python3-pytest-xdist python3-pytz python3-roman-numerals 131s python3-setuptools-scm python3-snowballstemmer python3-sphinx 131s python3-sphinx-autoapi python3-sphinx-autodoc-typehints 131s python3-sphinxcontrib.autoprogram python3-stubserver python3-tz 131s python3-wdlparse python3-werkzeug python3-wheel python3.13-doc python3.14 131s python3.14-minimal runc sgml-base sphinx-common sphinx-rtd-theme-common 131s xml-core 131s 0 upgraded, 98 newly installed, 0 to remove and 0 not upgraded. 131s Need to get 177 MB of archives. 131s After this operation, 665 MB of additional disk space will be used. 131s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-lato all 2.015-1build1 [2779 kB] 131s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 131s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.2-1 [2563 kB] 131s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 m4 amd64 1.4.20-2 [217 kB] 131s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 autoconf all 2.72-3.1ubuntu1 [384 kB] 131s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 autotools-dev all 20240727.1 [43.4 kB] 131s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 automake all 1:1.18.1-3build1 [582 kB] 131s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 autopoint all 0.23.2-1 [620 kB] 131s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB] 131s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB] 131s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [12.9 MB] 131s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-12ubuntu1 [1034 B] 131s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B] 131s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB] 131s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 15.2.0-12ubuntu1 [47.4 kB] 131s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 15.2.0-12ubuntu1 [29.5 kB] 131s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 15.2.0-12ubuntu1 [3070 kB] 132s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 15.2.0-12ubuntu1 [1360 kB] 132s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 15.2.0-12ubuntu1 [2757 kB] 132s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 15.2.0-12ubuntu1 [1210 kB] 133s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 15.2.0-12ubuntu1 [1685 kB] 133s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 15.2.0-12ubuntu1 [153 kB] 133s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-12ubuntu1 [2866 kB] 133s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [25.4 MB] 134s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-12ubuntu1 [530 kB] 134s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B] 134s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B] 134s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-12ubuntu1 [2553 kB] 134s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [14.4 MB] 134s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-12ubuntu1 [25.3 kB] 134s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B] 134s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B] 134s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B] 134s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 runc amd64 1.4.0-0ubuntu1 [9828 kB] 134s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 containerd amd64 2.2.1-0ubuntu1 [28.0 MB] 135s Get:36 http://ftpmaster.internal/ubuntu resolute/universe amd64 cwl-utils all 0.40-1 [2578 B] 135s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-defusedxml all 0.7.1-3build1 [42.4 kB] 135s Get:38 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-junit.xml all 1.9-6 [9062 B] 135s Get:39 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 2.1.0-2 [6962 B] 135s Get:40 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-2 [21.1 kB] 135s Get:41 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest all 9.0.2-2 [277 kB] 135s Get:42 http://ftpmaster.internal/ubuntu resolute/universe amd64 cwltest all 2.6.20251216093331-1 [29.1 kB] 135s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 135s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB] 135s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 135s Get:46 http://ftpmaster.internal/ubuntu resolute/universe amd64 cwltool-doc all 3.1.20251031082601-1 [332 kB] 135s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 135s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libtool all 2.5.4-9 [169 kB] 135s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 dh-autoreconf all 21 [12.5 kB] 135s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 135s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 135s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 135s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 debugedit amd64 1:5.2-3 [49.9 kB] 135s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 dwz amd64 0.16-2 [115 kB] 135s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 gettext amd64 0.23.2-1 [1019 kB] 135s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 135s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 po-debconf all 1.0.22 [215 kB] 135s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 debhelper all 13.28ubuntu1 [916 kB] 135s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 dh-python all 7.20260125 [122 kB] 135s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 docker.io amd64 29.1.3-0ubuntu1 [35.5 MB] 136s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 136s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19build1 [20.3 kB] 136s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 docutils-common all 0.22.4+dfsg-1 [130 kB] 136s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-underscore all 1.13.7~dfsg+~1.13.0-1 [86.4 kB] 136s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 libjson-perl all 4.10000-1 [81.9 kB] 137s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 137s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 pybuild-plugin-autopkgtest all 7.20260125 [1744 B] 137s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 137s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-wheel all 0.46.1-2 [22.1 kB] 137s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-build all 1.2.2-5 [30.9 kB] 137s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 137s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 pybuild-plugin-pyproject all 7.20260125 [1712 B] 137s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.2-1 [816 kB] 137s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-all amd64 3.13.9-3 [890 B] 137s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-antlr4 all 4.9.2-1build1 [99.1 kB] 137s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-astroid all 4.0.2-1ubuntu1 [172 kB] 137s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-doc all 3.13.11-1 [14.3 MB] 137s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-doc all 3.13.9-3 [11.1 kB] 137s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-roman-numerals all 4.1.0-1 [8660 B] 137s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-docutils all 0.22.4+dfsg-1 [439 kB] 137s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-execnet all 2.1.1-1build1 [33.5 kB] 137s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-imagesize all 1.4.1-1build1 [6900 B] 137s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-werkzeug all 3.1.5-1 [170 kB] 137s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest-httpserver all 1.1.3-1 [19.1 kB] 137s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest-timeout all 2.4.0-2 [22.5 kB] 137s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest-xdist all 3.8.0-4 [34.7 kB] 137s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytz all 2025.2-5 [32.4 kB] 137s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-setuptools-scm all 8.2.1-4 [32.8 kB] 137s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-snowballstemmer all 3.0.1-1 [65.9 kB] 137s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 sphinx-common all 8.2.3-12 [657 kB] 137s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-alabaster all 0.7.16-0.1build1 [18.6 kB] 137s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-sphinx all 8.2.3-12 [483 kB] 137s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sphinx-autoapi all 3.6.1-1 [102 kB] 137s Get:94 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sphinx-autodoc-typehints all 3.5.2-1 [22.7 kB] 137s Get:95 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sphinxcontrib.autoprogram all 0.1.9-1build1 [9752 B] 137s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-stubserver all 1.1-4build1 [7994 B] 137s Get:97 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-tz all 2025.2-5 [1760 B] 138s Get:98 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-wdlparse all 0.1.0-3build1 [71.0 kB] 138s Preconfiguring packages ... 138s Fetched 177 MB in 7s (26.2 MB/s) 138s Selecting previously unselected package fonts-lato. 138s (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 ... 132552 files and directories currently installed.) 138s Preparing to unpack .../00-fonts-lato_2.015-1build1_all.deb ... 138s Unpacking fonts-lato (2.015-1build1) ... 138s Selecting previously unselected package libpython3.14-minimal:amd64. 138s Preparing to unpack .../01-libpython3.14-minimal_3.14.2-1_amd64.deb ... 138s Unpacking libpython3.14-minimal:amd64 (3.14.2-1) ... 138s Selecting previously unselected package python3.14-minimal. 138s Preparing to unpack .../02-python3.14-minimal_3.14.2-1_amd64.deb ... 138s Unpacking python3.14-minimal (3.14.2-1) ... 138s Selecting previously unselected package m4. 138s Preparing to unpack .../03-m4_1.4.20-2_amd64.deb ... 138s Unpacking m4 (1.4.20-2) ... 138s Selecting previously unselected package autoconf. 138s Preparing to unpack .../04-autoconf_2.72-3.1ubuntu1_all.deb ... 138s Unpacking autoconf (2.72-3.1ubuntu1) ... 138s Selecting previously unselected package autotools-dev. 138s Preparing to unpack .../05-autotools-dev_20240727.1_all.deb ... 138s Unpacking autotools-dev (20240727.1) ... 138s Selecting previously unselected package automake. 138s Preparing to unpack .../06-automake_1%3a1.18.1-3build1_all.deb ... 138s Unpacking automake (1:1.18.1-3build1) ... 138s Selecting previously unselected package autopoint. 138s Preparing to unpack .../07-autopoint_0.23.2-1_all.deb ... 138s Unpacking autopoint (0.23.2-1) ... 138s Selecting previously unselected package libisl23:amd64. 138s Preparing to unpack .../08-libisl23_0.27-1build1_amd64.deb ... 138s Unpacking libisl23:amd64 (0.27-1build1) ... 138s Selecting previously unselected package libmpc3:amd64. 138s Preparing to unpack .../09-libmpc3_1.3.1-2_amd64.deb ... 138s Unpacking libmpc3:amd64 (1.3.1-2) ... 138s Selecting previously unselected package cpp-15-x86-64-linux-gnu. 138s Preparing to unpack .../10-cpp-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 138s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 138s Selecting previously unselected package cpp-15. 138s Preparing to unpack .../11-cpp-15_15.2.0-12ubuntu1_amd64.deb ... 138s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 138s Selecting previously unselected package cpp-x86-64-linux-gnu. 138s Preparing to unpack .../12-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 138s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 138s Selecting previously unselected package cpp. 138s Preparing to unpack .../13-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ... 138s Unpacking cpp (4:15.2.0-4ubuntu1) ... 138s Selecting previously unselected package libcc1-0:amd64. 138s Preparing to unpack .../14-libcc1-0_15.2.0-12ubuntu1_amd64.deb ... 138s Unpacking libcc1-0:amd64 (15.2.0-12ubuntu1) ... 138s Selecting previously unselected package libitm1:amd64. 138s Preparing to unpack .../15-libitm1_15.2.0-12ubuntu1_amd64.deb ... 138s Unpacking libitm1:amd64 (15.2.0-12ubuntu1) ... 138s Selecting previously unselected package libasan8:amd64. 138s Preparing to unpack .../16-libasan8_15.2.0-12ubuntu1_amd64.deb ... 138s Unpacking libasan8:amd64 (15.2.0-12ubuntu1) ... 138s Selecting previously unselected package liblsan0:amd64. 138s Preparing to unpack .../17-liblsan0_15.2.0-12ubuntu1_amd64.deb ... 138s Unpacking liblsan0:amd64 (15.2.0-12ubuntu1) ... 138s Selecting previously unselected package libtsan2:amd64. 138s Preparing to unpack .../18-libtsan2_15.2.0-12ubuntu1_amd64.deb ... 138s Unpacking libtsan2:amd64 (15.2.0-12ubuntu1) ... 138s Selecting previously unselected package libubsan1:amd64. 138s Preparing to unpack .../19-libubsan1_15.2.0-12ubuntu1_amd64.deb ... 138s Unpacking libubsan1:amd64 (15.2.0-12ubuntu1) ... 138s Selecting previously unselected package libhwasan0:amd64. 138s Preparing to unpack .../20-libhwasan0_15.2.0-12ubuntu1_amd64.deb ... 138s Unpacking libhwasan0:amd64 (15.2.0-12ubuntu1) ... 139s Selecting previously unselected package libquadmath0:amd64. 139s Preparing to unpack .../21-libquadmath0_15.2.0-12ubuntu1_amd64.deb ... 139s Unpacking libquadmath0:amd64 (15.2.0-12ubuntu1) ... 139s Selecting previously unselected package libgcc-15-dev:amd64. 139s Preparing to unpack .../22-libgcc-15-dev_15.2.0-12ubuntu1_amd64.deb ... 139s Unpacking libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ... 139s Selecting previously unselected package gcc-15-x86-64-linux-gnu. 139s Preparing to unpack .../23-gcc-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 139s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 139s Selecting previously unselected package gcc-15. 139s Preparing to unpack .../24-gcc-15_15.2.0-12ubuntu1_amd64.deb ... 139s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 139s Selecting previously unselected package gcc-x86-64-linux-gnu. 139s Preparing to unpack .../25-gcc-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 139s Unpacking gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 139s Selecting previously unselected package gcc. 139s Preparing to unpack .../26-gcc_4%3a15.2.0-4ubuntu1_amd64.deb ... 139s Unpacking gcc (4:15.2.0-4ubuntu1) ... 139s Selecting previously unselected package libstdc++-15-dev:amd64. 139s Preparing to unpack .../27-libstdc++-15-dev_15.2.0-12ubuntu1_amd64.deb ... 139s Unpacking libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ... 139s Selecting previously unselected package g++-15-x86-64-linux-gnu. 139s Preparing to unpack .../28-g++-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 139s Unpacking g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 139s Selecting previously unselected package g++-15. 139s Preparing to unpack .../29-g++-15_15.2.0-12ubuntu1_amd64.deb ... 139s Unpacking g++-15 (15.2.0-12ubuntu1) ... 139s Selecting previously unselected package g++-x86-64-linux-gnu. 139s Preparing to unpack .../30-g++-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 139s Unpacking g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 139s Selecting previously unselected package g++. 139s Preparing to unpack .../31-g++_4%3a15.2.0-4ubuntu1_amd64.deb ... 139s Unpacking g++ (4:15.2.0-4ubuntu1) ... 139s Selecting previously unselected package build-essential. 139s Preparing to unpack .../32-build-essential_12.12ubuntu2_amd64.deb ... 139s Unpacking build-essential (12.12ubuntu2) ... 139s Selecting previously unselected package runc. 139s Preparing to unpack .../33-runc_1.4.0-0ubuntu1_amd64.deb ... 139s Unpacking runc (1.4.0-0ubuntu1) ... 139s Selecting previously unselected package containerd. 139s Preparing to unpack .../34-containerd_2.2.1-0ubuntu1_amd64.deb ... 139s Unpacking containerd (2.2.1-0ubuntu1) ... 140s Selecting previously unselected package cwl-utils. 140s Preparing to unpack .../35-cwl-utils_0.40-1_all.deb ... 140s Unpacking cwl-utils (0.40-1) ... 140s Selecting previously unselected package python3-defusedxml. 140s Preparing to unpack .../36-python3-defusedxml_0.7.1-3build1_all.deb ... 140s Unpacking python3-defusedxml (0.7.1-3build1) ... 140s Selecting previously unselected package python3-junit.xml. 140s Preparing to unpack .../37-python3-junit.xml_1.9-6_all.deb ... 140s Unpacking python3-junit.xml (1.9-6) ... 140s Selecting previously unselected package python3-iniconfig. 140s Preparing to unpack .../38-python3-iniconfig_2.1.0-2_all.deb ... 140s Unpacking python3-iniconfig (2.1.0-2) ... 140s Selecting previously unselected package python3-pluggy. 140s Preparing to unpack .../39-python3-pluggy_1.6.0-2_all.deb ... 140s Unpacking python3-pluggy (1.6.0-2) ... 140s Selecting previously unselected package python3-pytest. 140s Preparing to unpack .../40-python3-pytest_9.0.2-2_all.deb ... 140s Unpacking python3-pytest (9.0.2-2) ... 140s Selecting previously unselected package cwltest. 140s Preparing to unpack .../41-cwltest_2.6.20251216093331-1_all.deb ... 140s Unpacking cwltest (2.6.20251216093331-1) ... 140s Selecting previously unselected package libjs-jquery. 140s Preparing to unpack .../42-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 140s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 140s Selecting previously unselected package fonts-font-awesome. 140s Preparing to unpack .../43-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1build1_all.deb ... 140s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 140s Selecting previously unselected package sphinx-rtd-theme-common. 140s Preparing to unpack .../44-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 140s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 140s Selecting previously unselected package cwltool-doc. 140s Preparing to unpack .../45-cwltool-doc_3.1.20251031082601-1_all.deb ... 140s Unpacking cwltool-doc (3.1.20251031082601-1) ... 140s Selecting previously unselected package libdebhelper-perl. 140s Preparing to unpack .../46-libdebhelper-perl_13.28ubuntu1_all.deb ... 140s Unpacking libdebhelper-perl (13.28ubuntu1) ... 140s Selecting previously unselected package libtool. 140s Preparing to unpack .../47-libtool_2.5.4-9_all.deb ... 140s Unpacking libtool (2.5.4-9) ... 140s Selecting previously unselected package dh-autoreconf. 140s Preparing to unpack .../48-dh-autoreconf_21_all.deb ... 140s Unpacking dh-autoreconf (21) ... 140s Selecting previously unselected package libarchive-zip-perl. 140s Preparing to unpack .../49-libarchive-zip-perl_1.68-1_all.deb ... 140s Unpacking libarchive-zip-perl (1.68-1) ... 140s Selecting previously unselected package libfile-stripnondeterminism-perl. 140s Preparing to unpack .../50-libfile-stripnondeterminism-perl_1.15.0-1build1_all.deb ... 140s Unpacking libfile-stripnondeterminism-perl (1.15.0-1build1) ... 140s Selecting previously unselected package dh-strip-nondeterminism. 140s Preparing to unpack .../51-dh-strip-nondeterminism_1.15.0-1build1_all.deb ... 140s Unpacking dh-strip-nondeterminism (1.15.0-1build1) ... 140s Selecting previously unselected package debugedit. 140s Preparing to unpack .../52-debugedit_1%3a5.2-3_amd64.deb ... 140s Unpacking debugedit (1:5.2-3) ... 140s Selecting previously unselected package dwz. 140s Preparing to unpack .../53-dwz_0.16-2_amd64.deb ... 140s Unpacking dwz (0.16-2) ... 140s Selecting previously unselected package gettext. 140s Preparing to unpack .../54-gettext_0.23.2-1_amd64.deb ... 140s Unpacking gettext (0.23.2-1) ... 140s Selecting previously unselected package intltool-debian. 140s Preparing to unpack .../55-intltool-debian_0.35.0+20060710.6build1_all.deb ... 140s Unpacking intltool-debian (0.35.0+20060710.6build1) ... 140s Selecting previously unselected package po-debconf. 140s Preparing to unpack .../56-po-debconf_1.0.22_all.deb ... 140s Unpacking po-debconf (1.0.22) ... 140s Selecting previously unselected package debhelper. 140s Preparing to unpack .../57-debhelper_13.28ubuntu1_all.deb ... 140s Unpacking debhelper (13.28ubuntu1) ... 140s Selecting previously unselected package dh-python. 140s Preparing to unpack .../58-dh-python_7.20260125_all.deb ... 140s Unpacking dh-python (7.20260125) ... 140s Selecting previously unselected package docker.io. 140s Preparing to unpack .../59-docker.io_29.1.3-0ubuntu1_amd64.deb ... 140s Unpacking docker.io (29.1.3-0ubuntu1) ... 140s Selecting previously unselected package sgml-base. 140s Preparing to unpack .../60-sgml-base_1.31+nmu1_all.deb ... 140s Unpacking sgml-base (1.31+nmu1) ... 140s Selecting previously unselected package xml-core. 140s Preparing to unpack .../61-xml-core_0.19build1_all.deb ... 140s Unpacking xml-core (0.19build1) ... 140s Selecting previously unselected package docutils-common. 140s Preparing to unpack .../62-docutils-common_0.22.4+dfsg-1_all.deb ... 140s Unpacking docutils-common (0.22.4+dfsg-1) ... 140s Selecting previously unselected package libjs-underscore. 140s Preparing to unpack .../63-libjs-underscore_1.13.7~dfsg+~1.13.0-1_all.deb ... 140s Unpacking libjs-underscore (1.13.7~dfsg+~1.13.0-1) ... 140s Selecting previously unselected package libjson-perl. 140s Preparing to unpack .../64-libjson-perl_4.10000-1_all.deb ... 140s Unpacking libjson-perl (4.10000-1) ... 140s Selecting previously unselected package libpython3.14-stdlib:amd64. 140s Preparing to unpack .../65-libpython3.14-stdlib_3.14.2-1_amd64.deb ... 140s Unpacking libpython3.14-stdlib:amd64 (3.14.2-1) ... 140s Selecting previously unselected package pybuild-plugin-autopkgtest. 140s Preparing to unpack .../66-pybuild-plugin-autopkgtest_7.20260125_all.deb ... 140s Unpacking pybuild-plugin-autopkgtest (7.20260125) ... 140s Selecting previously unselected package python3-pyproject-hooks. 140s Preparing to unpack .../67-python3-pyproject-hooks_1.2.0-1_all.deb ... 140s Unpacking python3-pyproject-hooks (1.2.0-1) ... 140s Selecting previously unselected package python3-wheel. 140s Preparing to unpack .../68-python3-wheel_0.46.1-2_all.deb ... 140s Unpacking python3-wheel (0.46.1-2) ... 140s Selecting previously unselected package python3-build. 140s Preparing to unpack .../69-python3-build_1.2.2-5_all.deb ... 140s Unpacking python3-build (1.2.2-5) ... 141s Selecting previously unselected package python3-installer. 141s Preparing to unpack .../70-python3-installer_0.7.0+dfsg1-3_all.deb ... 141s Unpacking python3-installer (0.7.0+dfsg1-3) ... 141s Selecting previously unselected package pybuild-plugin-pyproject. 141s Preparing to unpack .../71-pybuild-plugin-pyproject_7.20260125_all.deb ... 141s Unpacking pybuild-plugin-pyproject (7.20260125) ... 141s Selecting previously unselected package python3.14. 141s Preparing to unpack .../72-python3.14_3.14.2-1_amd64.deb ... 141s Unpacking python3.14 (3.14.2-1) ... 141s Selecting previously unselected package python3-all. 141s Preparing to unpack .../73-python3-all_3.13.9-3_amd64.deb ... 141s Unpacking python3-all (3.13.9-3) ... 141s Selecting previously unselected package python3-antlr4. 141s Preparing to unpack .../74-python3-antlr4_4.9.2-1build1_all.deb ... 141s Unpacking python3-antlr4 (4.9.2-1build1) ... 141s Selecting previously unselected package python3-astroid. 141s Preparing to unpack .../75-python3-astroid_4.0.2-1ubuntu1_all.deb ... 141s Unpacking python3-astroid (4.0.2-1ubuntu1) ... 141s Selecting previously unselected package python3.13-doc. 141s Preparing to unpack .../76-python3.13-doc_3.13.11-1_all.deb ... 141s Unpacking python3.13-doc (3.13.11-1) ... 141s Selecting previously unselected package python3-doc. 141s Preparing to unpack .../77-python3-doc_3.13.9-3_all.deb ... 141s Unpacking python3-doc (3.13.9-3) ... 141s Selecting previously unselected package python3-roman-numerals. 141s Preparing to unpack .../78-python3-roman-numerals_4.1.0-1_all.deb ... 141s Unpacking python3-roman-numerals (4.1.0-1) ... 141s Selecting previously unselected package python3-docutils. 141s Preparing to unpack .../79-python3-docutils_0.22.4+dfsg-1_all.deb ... 141s Unpacking python3-docutils (0.22.4+dfsg-1) ... 141s Selecting previously unselected package python3-execnet. 141s Preparing to unpack .../80-python3-execnet_2.1.1-1build1_all.deb ... 141s Unpacking python3-execnet (2.1.1-1build1) ... 141s Selecting previously unselected package python3-imagesize. 141s Preparing to unpack .../81-python3-imagesize_1.4.1-1build1_all.deb ... 141s Unpacking python3-imagesize (1.4.1-1build1) ... 141s Selecting previously unselected package python3-werkzeug. 141s Preparing to unpack .../82-python3-werkzeug_3.1.5-1_all.deb ... 141s Unpacking python3-werkzeug (3.1.5-1) ... 141s Selecting previously unselected package python3-pytest-httpserver. 141s Preparing to unpack .../83-python3-pytest-httpserver_1.1.3-1_all.deb ... 141s Unpacking python3-pytest-httpserver (1.1.3-1) ... 141s Selecting previously unselected package python3-pytest-timeout. 141s Preparing to unpack .../84-python3-pytest-timeout_2.4.0-2_all.deb ... 141s Unpacking python3-pytest-timeout (2.4.0-2) ... 141s Selecting previously unselected package python3-pytest-xdist. 141s Preparing to unpack .../85-python3-pytest-xdist_3.8.0-4_all.deb ... 141s Unpacking python3-pytest-xdist (3.8.0-4) ... 141s Selecting previously unselected package python3-pytz. 141s Preparing to unpack .../86-python3-pytz_2025.2-5_all.deb ... 141s Unpacking python3-pytz (2025.2-5) ... 141s Selecting previously unselected package python3-setuptools-scm. 141s Preparing to unpack .../87-python3-setuptools-scm_8.2.1-4_all.deb ... 141s Unpacking python3-setuptools-scm (8.2.1-4) ... 141s Selecting previously unselected package python3-snowballstemmer. 141s Preparing to unpack .../88-python3-snowballstemmer_3.0.1-1_all.deb ... 141s Unpacking python3-snowballstemmer (3.0.1-1) ... 141s Selecting previously unselected package sphinx-common. 141s Preparing to unpack .../89-sphinx-common_8.2.3-12_all.deb ... 141s Unpacking sphinx-common (8.2.3-12) ... 141s Selecting previously unselected package python3-alabaster. 141s Preparing to unpack .../90-python3-alabaster_0.7.16-0.1build1_all.deb ... 141s Unpacking python3-alabaster (0.7.16-0.1build1) ... 141s Selecting previously unselected package python3-sphinx. 141s Preparing to unpack .../91-python3-sphinx_8.2.3-12_all.deb ... 141s Unpacking python3-sphinx (8.2.3-12) ... 141s Selecting previously unselected package python3-sphinx-autoapi. 141s Preparing to unpack .../92-python3-sphinx-autoapi_3.6.1-1_all.deb ... 141s Unpacking python3-sphinx-autoapi (3.6.1-1) ... 141s Selecting previously unselected package python3-sphinx-autodoc-typehints. 141s Preparing to unpack .../93-python3-sphinx-autodoc-typehints_3.5.2-1_all.deb ... 141s Unpacking python3-sphinx-autodoc-typehints (3.5.2-1) ... 141s Selecting previously unselected package python3-sphinxcontrib.autoprogram. 141s Preparing to unpack .../94-python3-sphinxcontrib.autoprogram_0.1.9-1build1_all.deb ... 141s Unpacking python3-sphinxcontrib.autoprogram (0.1.9-1build1) ... 141s Selecting previously unselected package python3-stubserver. 141s Preparing to unpack .../95-python3-stubserver_1.1-4build1_all.deb ... 141s Unpacking python3-stubserver (1.1-4build1) ... 141s Selecting previously unselected package python3-tz. 141s Preparing to unpack .../96-python3-tz_2025.2-5_all.deb ... 141s Unpacking python3-tz (2025.2-5) ... 141s Selecting previously unselected package python3-wdlparse. 141s Preparing to unpack .../97-python3-wdlparse_0.1.0-3build1_all.deb ... 141s Unpacking python3-wdlparse (0.1.0-3build1) ... 141s Setting up dh-python (7.20260125) ... 141s Setting up python3-iniconfig (2.1.0-2) ... 141s Setting up python3-antlr4 (4.9.2-1build1) ... 142s Setting up gettext (0.23.2-1) ... 142s Setting up fonts-lato (2.015-1build1) ... 142s Setting up python3-defusedxml (0.7.1-3build1) ... 142s Setting up libarchive-zip-perl (1.68-1) ... 142s Setting up python3-alabaster (0.7.16-0.1build1) ... 142s Setting up python3-junit.xml (1.9-6) ... 142s Setting up libdebhelper-perl (13.28ubuntu1) ... 142s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 142s Setting up m4 (1.4.20-2) ... 142s Setting up python3-pytz (2025.2-5) ... 142s Setting up python3-wheel (0.46.1-2) ... 142s Setting up python3-setuptools-scm (8.2.1-4) ... 142s Setting up python3-tz (2025.2-5) ... 142s Setting up runc (1.4.0-0ubuntu1) ... 142s Setting up intltool-debian (0.35.0+20060710.6build1) ... 142s Setting up python3-stubserver (1.1-4build1) ... 142s Setting up autotools-dev (20240727.1) ... 142s Setting up python3-pyproject-hooks (1.2.0-1) ... 142s Setting up python3-snowballstemmer (3.0.1-1) ... 143s Setting up python3-werkzeug (3.1.5-1) ... 143s Setting up libquadmath0:amd64 (15.2.0-12ubuntu1) ... 143s Setting up cwl-utils (0.40-1) ... 143s Setting up libmpc3:amd64 (1.3.1-2) ... 143s Setting up autopoint (0.23.2-1) ... 143s Setting up python3-installer (0.7.0+dfsg1-3) ... 143s Setting up autoconf (2.72-3.1ubuntu1) ... 143s Setting up python3-pluggy (1.6.0-2) ... 143s Setting up libubsan1:amd64 (15.2.0-12ubuntu1) ... 143s Setting up dwz (0.16-2) ... 143s Setting up python3-astroid (4.0.2-1ubuntu1) ... 143s Setting up libhwasan0:amd64 (15.2.0-12ubuntu1) ... 143s Setting up libasan8:amd64 (15.2.0-12ubuntu1) ... 144s Setting up libjson-perl (4.10000-1) ... 144s Setting up python3-pytest-httpserver (1.1.3-1) ... 144s Setting up debugedit (1:5.2-3) ... 144s Setting up python3-roman-numerals (4.1.0-1) ... 144s Setting up sgml-base (1.31+nmu1) ... 144s Setting up libtsan2:amd64 (15.2.0-12ubuntu1) ... 144s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 144s Setting up libisl23:amd64 (0.27-1build1) ... 144s Setting up python3-build (1.2.2-5) ... 144s Setting up containerd (2.2.1-0ubuntu1) ... 144s Created symlink '/etc/systemd/system/multi-user.target.wants/containerd.service' → '/usr/lib/systemd/system/containerd.service'. 144s Setting up python3-execnet (2.1.1-1build1) ... 144s Setting up python3-wdlparse (0.1.0-3build1) ... 145s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 145s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 145s Setting up python3.14-minimal (3.14.2-1) ... 145s Setting up libcc1-0:amd64 (15.2.0-12ubuntu1) ... 145s Setting up liblsan0:amd64 (15.2.0-12ubuntu1) ... 145s Setting up libitm1:amd64 (15.2.0-12ubuntu1) ... 145s Setting up libjs-underscore (1.13.7~dfsg+~1.13.0-1) ... 145s Setting up python3-imagesize (1.4.1-1build1) ... 145s Setting up automake (1:1.18.1-3build1) ... 145s update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode 145s Setting up libfile-stripnondeterminism-perl (1.15.0-1build1) ... 145s Setting up cwltool-doc (3.1.20251031082601-1) ... 145s Setting up libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ... 145s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 145s Setting up pybuild-plugin-pyproject (7.20260125) ... 145s Setting up python3-pytest (9.0.2-2) ... 146s Setting up po-debconf (1.0.22) ... 146s Setting up docker.io (29.1.3-0ubuntu1) ... 146s Created symlink '/etc/systemd/system/multi-user.target.wants/docker.service' → '/usr/lib/systemd/system/docker.service'. 146s Created symlink '/etc/systemd/system/sockets.target.wants/docker.socket' → '/usr/lib/systemd/system/docker.socket'. 146s Setting up cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 146s Setting up gcc-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 146s Setting up python3.13-doc (3.13.11-1) ... 146s Setting up libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ... 146s Setting up sphinx-common (8.2.3-12) ... 146s Setting up cwltest (2.6.20251216093331-1) ... 146s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 146s Setting up cpp-15 (15.2.0-12ubuntu1) ... 146s Setting up xml-core (0.19build1) ... 146s Setting up python3.14 (3.14.2-1) ... 147s Setting up python3-doc (3.13.9-3) ... 147s Setting up cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 147s Setting up g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 147s Setting up python3-pytest-xdist (3.8.0-4) ... 147s Setting up python3-pytest-timeout (2.4.0-2) ... 147s Setting up gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 147s Setting up python3-all (3.13.9-3) ... 147s Setting up gcc-15 (15.2.0-12ubuntu1) ... 147s Setting up cpp (4:15.2.0-4ubuntu1) ... 147s Setting up g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 147s Setting up g++-15 (15.2.0-12ubuntu1) ... 147s Setting up libtool (2.5.4-9) ... 147s Setting up gcc (4:15.2.0-4ubuntu1) ... 147s Setting up dh-autoreconf (21) ... 147s Setting up g++ (4:15.2.0-4ubuntu1) ... 147s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 147s Setting up build-essential (12.12ubuntu2) ... 147s Setting up debhelper (13.28ubuntu1) ... 147s Setting up pybuild-plugin-autopkgtest (7.20260125) ... 147s Processing triggers for install-info (7.2-5) ... 147s Processing triggers for fontconfig (2.17.1-3ubuntu1) ... 147s Processing triggers for libc-bin (2.42-2ubuntu4) ... 147s Processing triggers for systemd (259-1ubuntu2) ... 147s Processing triggers for man-db (2.13.1-1) ... 148s Processing triggers for sgml-base (1.31+nmu1) ... 148s Setting up docutils-common (0.22.4+dfsg-1) ... 148s Processing triggers for sgml-base (1.31+nmu1) ... 148s Setting up python3-docutils (0.22.4+dfsg-1) ... 149s Setting up python3-sphinx (8.2.3-12) ... 150s Setting up python3-sphinx-autodoc-typehints (3.5.2-1) ... 150s Setting up python3-sphinx-autoapi (3.6.1-1) ... 150s Setting up python3-sphinxcontrib.autoprogram (0.1.9-1build1) ... 151s autopkgtest [23:42:28]: test pybuild-autopkgtest: pybuild-autopkgtest 151s autopkgtest [23:42:28]: test pybuild-autopkgtest: [----------------------- 152s pybuild-autopkgtest 152s I: pybuild base:384: cd /tmp/autopkgtest.IiScC1/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.IiScC1/autopkgtest_tmp/build 155s configfile: setup.cfg 155s plugins: timeout-2.4.0, typeguard-4.4.4, xdist-3.8.0, cwltest-2.6.20251216093331, pytest_httpserver-1.1.3 155s created: 4/4 workers 155s 4 workers [375 items] 155s 155s scheduling tests via LoadScopeScheduling 155s 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 jobStores/jobStoreTest.py::FileJobStoreTest::testBatchCreate <- ../../../../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 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::AWSJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 0%] 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] [ 0%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testConfigEquality <- ../../../../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 [gw2] [ 1%] 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 [gw2] [ 1%] 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 [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 [gw2] [ 2%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::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 [gw1] [ 2%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::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 [gw1] [ 2%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testImportFtpFile <- ../../../../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 jobStores/jobStoreTest.py::AWSJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 3%] 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 [gw2] [ 3%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 3%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testInitialState <- ../../../../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::testJobCreation <- ../../../../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::AWSJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 4%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 4%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testJobDeletions <- ../../../../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 [gw1] [ 4%] 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] [ 5%] 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] [ 5%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testOverlargeJob <- ../../../../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::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 5%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportFtpFile <- ../../../../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 [gw2] [ 5%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportHttpFile <- ../../../../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 [gw2] [ 6%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testInitialState <- ../../../../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 [gw2] [ 6%] 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] [ 6%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testPartialReadFromStream <- ../../../../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] [ 6%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testPerJobFiles <- ../../../../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 jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 7%] 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 [gw2] [ 7%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobDeletions <- ../../../../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 [gw2] [ 8%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobLoadEquality <- ../../../../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 [gw2] [ 8%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testPartialReadFromStream <- ../../../../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 [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] [ 8%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testPersistantFilesToDelete <- ../../../../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 [gw1] [ 9%] 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] [ 9%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../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 [gw2] [ 9%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../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 [gw2] [ 9%] 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 [gw2] [ 10%] 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 [gw1] [ 10%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testSharedFiles <- ../../../../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] [ 10%] 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 [gw1] [ 10%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testUpdateBehavior <- ../../../../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 [gw1] [ 11%] 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 [gw1] [ 11%] 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 [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 [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_onemib <- ../../../../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_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 12%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testWriteLogFiles <- ../../../../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 jobStores/jobStoreTest.py::GoogleJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw2] [ 12%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 155s [gw1] [ 13%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::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_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 13%] 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] [ 13%] 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 [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] [ 14%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 14%] 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::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 14%] 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] [ 14%] 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::AWSJobStoreTest::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_activated__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_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 15%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::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_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw1] [ 15%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 16%] 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 jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 16%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw1] [ 16%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::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_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 [gw2] [ 16%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw1] [ 17%] 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::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw2] [ 17%] 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] [ 17%] 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 jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw1] [ 17%] 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 [gw1] [ 18%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::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_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 jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 155s [gw1] [ 18%] 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 [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 156s jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 156s [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 156s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 156s [gw0] [ 22%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 156s jobStores/jobStoreTest.py::FileJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 156s [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 156s 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 156s [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 156s 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 [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 [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] [ 25%] 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] [ 26%] 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 [gw0] [ 27%] 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] [ 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 [gw3] [ 28%] PASSED batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_time <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 157s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 157s [gw0] [ 29%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 158s jobStores/jobStoreTest.py::FileJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.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 161s 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 [gw1] [ 30%] FAILED docs/scriptsTest.py::ToilDocumentationTest::testDocker <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 164s docs/scriptsTest.py::ToilDocumentationTest::testDynamic <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 165s [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 165s [gw2] [ 30%] FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_FORGO <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 167s lib/dockerTest.py::TestDocker::testDockerClean_CRx_STOP <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.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 169s lib/dockerTest.py::TestDocker::testDockerClean_CRx_RM <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 172s [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 173s [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 173s [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 177s [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 178s [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 178s [gw2] [ 31%] FAILED lib/dockerTest.py::TestDocker::testDockerPipeChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 180s lib/dockerTest.py::TestDocker::testDockerPipeChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 180s [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 180s [gw3] [ 31%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 181s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 181s [gw1] [ 31%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testDynamic <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 183s docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 183s [gw2] [ 32%] FAILED lib/dockerTest.py::TestDocker::testDockerPipeChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 183s lib/dockerTest.py::TestDocker::testNonCachingDockerChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 183s [gw3] [ 32%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 184s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 184s [gw1] [ 32%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 185s docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 185s [gw3] [ 32%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 186s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 186s [gw0] [ 33%] 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] [ 33%] 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] [ 33%] FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 188s lib/dockerTest.py::TestDocker::testNonCachingDockerChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 188s [gw3] [ 33%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 189s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 189s [gw1] [ 34%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 190s docs/scriptsTest.py::ToilDocumentationTest::testHelloworld <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 190s [gw3] [ 34%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 191s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 191s [gw2] [ 34%] FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 193s lib/dockerTest.py::TestDocker::testDockerLogs <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 193s [gw1] [ 34%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testHelloworld <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 196s docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 196s [gw1] [ 35%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 199s docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 199s [gw2] [ 35%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 199s lib/dockerTest.py::TestDocker::testDockerLogs_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 199s [gw1] [ 35%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 202s docs/scriptsTest.py::ToilDocumentationTest::testJobFunctions <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 202s [gw1] [ 36%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testJobFunctions <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 204s docs/scriptsTest.py::ToilDocumentationTest::testManaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 204s [gw2] [ 36%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 205s lib/dockerTest.py::TestDocker::testDockerLogs_Demux <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 205s [gw1] [ 36%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testManaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 208s docs/scriptsTest.py::ToilDocumentationTest::testManaging2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 208s [gw1] [ 36%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testManaging2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 208s docs/scriptsTest.py::ToilDocumentationTest::testPromises <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 208s [gw2] [ 37%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 210s lib/dockerTest.py::TestDocker::testDockerLogs_Demux_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 210s [gw1] [ 37%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testPromises <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 212s docs/scriptsTest.py::ToilDocumentationTest::testPromises2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 212s [gw2] [ 37%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 212s src/dockerCheckTest.py::DockerCheckTest::testApplianceParser <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 212s [gw2] [ 37%] PASSED src/dockerCheckTest.py::DockerCheckTest::testApplianceParser <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 216s src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 216s [gw2] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 216s src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 216s [gw2] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 216s src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 216s [gw2] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 217s src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 217s [gw2] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 217s src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 217s [gw2] [ 39%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 217s src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 217s [gw2] [ 39%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 217s src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 217s [gw2] [ 39%] PASSED src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 217s src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 217s [gw2] [ 40%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 217s src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 217s [gw2] [ 40%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 217s src/dockerCheckTest.py::DockerCheckTest::testToilQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 217s [gw2] [ 40%] PASSED src/dockerCheckTest.py::DockerCheckTest::testToilQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 217s provisioners/clusterScalerTest.py::ClusterScalerTest::testBetaInertia <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 217s [gw2] [ 40%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testBetaInertia <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 217s provisioners/clusterScalerTest.py::ClusterScalerTest::testMaxNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 217s [gw2] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testMaxNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 217s provisioners/clusterScalerTest.py::ClusterScalerTest::testMinNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 217s [gw2] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testMinNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 217s provisioners/clusterScalerTest.py::ClusterScalerTest::testNoLaunchingIfDeltaAlreadyMet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 217s [gw2] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testNoLaunchingIfDeltaAlreadyMet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 217s provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitIsSet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 217s [gw2] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitIsSet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitResponse <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s [gw2] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitResponse <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s provisioners/clusterScalerTest.py::ClusterScalerTest::testRounding <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s [gw2] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testRounding <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_large <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s [gw2] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_large <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_observed <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s [gw2] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_observed <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_small <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s [gw2] [ 43%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_small <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s server/serverTest.py::ToilWESServerWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 43%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 43%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [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 218s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 47%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 47%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 47%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [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 218s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [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 218s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s [gw2] [ 51%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 218s provisioners/clusterScalerTest.py::BinPackingTest::testAddingInitialNode <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s [gw2] [ 51%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testAddingInitialNode <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s provisioners/clusterScalerTest.py::BinPackingTest::testHighTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s [gw2] [ 51%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testHighTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s provisioners/clusterScalerTest.py::BinPackingTest::testJobTooLargeForAllNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s [gw2] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testJobTooLargeForAllNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s provisioners/clusterScalerTest.py::BinPackingTest::testLongRunningJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s [gw2] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testLongRunningJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s provisioners/clusterScalerTest.py::BinPackingTest::testLowTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s [gw2] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testLowTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s provisioners/clusterScalerTest.py::BinPackingTest::testPackingOneShape <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s [gw2] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testPackingOneShape <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s provisioners/clusterScalerTest.py::BinPackingTest::testPathologicalCase <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s [gw2] [ 53%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testPathologicalCase <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s provisioners/clusterScalerTest.py::BinPackingTest::testSorting <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s [gw2] [ 53%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testSorting <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s provisioners/clusterScalerTest.py::BinPackingTest::testZeroResourceJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s [gw2] [ 53%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testZeroResourceJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 218s utils/utilsTest.py::TestUtils::test_config_functionality <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 218s [gw2] [ 53%] PASSED utils/utilsTest.py::TestUtils::test_config_functionality <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 225s utils/utilsTest.py::TestUtils::testUtilsSort <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 225s [gw1] [ 54%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testPromises2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 228s docs/scriptsTest.py::ToilDocumentationTest::testQuickstart <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 228s [gw1] [ 54%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testQuickstart <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 236s docs/scriptsTest.py::ToilDocumentationTest::testRequirements <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 236s [gw1] [ 54%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testRequirements <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 239s docs/scriptsTest.py::ToilDocumentationTest::testStaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 239s [gw1] [ 54%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testStaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 249s docs/scriptsTest.py::ToilDocumentationTest::testStats <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 249s [gw0] [ 55%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s [gw0] [ 55%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s [gw0] [ 55%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s [gw0] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s [gw0] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s [gw0] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s [gw0] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s [gw0] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s [gw0] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s [gw0] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s [gw0] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s [gw0] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s [gw0] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::test_file_link_imports <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s [gw0] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_file_link_imports <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_does_not_leak_symlinks <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s [gw0] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_does_not_leak_symlinks <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_init_preserves_symlink_path <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s [gw0] [ 59%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_init_preserves_symlink_path <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::test_symlink_read_control <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s [gw0] [ 59%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_symlink_read_control <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s [gw0] [ 59%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s [gw0] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s [gw0] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s [gw0] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s [gw0] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s [gw0] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s [gw0] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s [gw0] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s [gw0] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s [gw0] [ 62%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s [gw0] [ 62%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s [gw0] [ 62%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s [gw0] [ 62%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 249s lib/test_url.py::TestURLAccess::test_get_url_access <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 249s [gw0] [ 63%] PASSED lib/test_url.py::TestURLAccess::test_get_url_access <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 249s lib/test_url.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 249s [gw0] [ 63%] SKIPPED lib/test_url.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 249s lib/test_url.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 249s [gw0] [ 63%] SKIPPED lib/test_url.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 249s lib/test_url.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 249s [gw0] [ 64%] SKIPPED lib/test_url.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 249s lib/test_url.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 249s [gw0] [ 64%] SKIPPED lib/test_url.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 249s lib/test_url.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 249s [gw0] [ 64%] SKIPPED lib/test_url.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 249s lib/url_plugin_test.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 249s [gw0] [ 64%] PASSED lib/url_plugin_test.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 249s lib/url_plugin_test.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 249s [gw0] [ 65%] PASSED lib/url_plugin_test.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 249s lib/url_plugin_test.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 249s [gw0] [ 65%] PASSED lib/url_plugin_test.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 249s lib/url_plugin_test.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 249s [gw0] [ 65%] PASSED lib/url_plugin_test.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 249s lib/url_plugin_test.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 249s [gw0] [ 65%] PASSED lib/url_plugin_test.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 249s lib/url_plugin_test.py::TestURLAccess::test_url_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 249s [gw0] [ 66%] PASSED lib/url_plugin_test.py::TestURLAccess::test_url_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 252s src/retainTempDirTest.py::TestCleanWorkDir::testNever <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 252s [gw0] [ 66%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testNever <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 255s src/retainTempDirTest.py::TestCleanWorkDir::testAlways <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 255s [gw0] [ 66%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testAlways <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 259s src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 259s [gw0] [ 66%] 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] [ 67%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithNoError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 263s src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 263s [gw1] [ 67%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testStats <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 263s src/miscTests.py::TestMisc::testIDStability <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 263s [gw1] [ 67%] PASSED src/miscTests.py::TestMisc::testIDStability <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 263s src/miscTests.py::TestMisc::test_atomic_install <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 263s [gw1] [ 68%] PASSED src/miscTests.py::TestMisc::test_atomic_install <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 263s src/miscTests.py::TestMisc::test_atomic_install_dev <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 263s [gw1] [ 68%] PASSED src/miscTests.py::TestMisc::test_atomic_install_dev <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 263s src/miscTests.py::TestMisc::test_atomic_context_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 263s [gw1] [ 68%] PASSED src/miscTests.py::TestMisc::test_atomic_context_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 263s src/miscTests.py::TestMisc::test_atomic_context_error <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 263s [gw1] [ 68%] PASSED src/miscTests.py::TestMisc::test_atomic_context_error <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 263s src/miscTests.py::TestMisc::test_call_command_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 263s [gw1] [ 69%] PASSED src/miscTests.py::TestMisc::test_call_command_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 263s src/miscTests.py::TestMisc::test_call_command_err <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 263s [gw1] [ 69%] PASSED src/miscTests.py::TestMisc::test_call_command_err <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 265s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 265s [gw2] [ 69%] PASSED utils/utilsTest.py::TestUtils::testUtilsSort <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 266s utils/utilsTest.py::TestUtils::testUnicodeSupport <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 266s [gw0] [ 69%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 266s src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithSuccess <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 268s [gw1] [ 70%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s [gw2] [ 70%] PASSED utils/utilsTest.py::TestUtils::testUnicodeSupport <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 268s utils/utilsTest.py::TestUtils::testGetPIDStatus <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 268s [gw0] [ 70%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithSuccess <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 268s lib/aws/test_utils.py::TagGenerationTest::test_build_tag <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 268s [gw0] [ 70%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_build_tag <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 268s lib/aws/test_utils.py::TagGenerationTest::test_build_tag_with_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 268s [gw0] [ 71%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_build_tag_with_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 268s lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 268s [gw0] [ 71%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 268s lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 268s [gw0] [ 71%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 268s lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 268s [gw0] [ 72%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 268s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s [gw0] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s [gw0] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s [gw0] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s [gw0] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s [gw0] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s [gw0] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s [gw0] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s [gw0] [ 74%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s [gw0] [ 74%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s [gw0] [ 74%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s src/resourceTest.py::TestResource::testStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 268s [gw0] [ 74%] PASSED src/resourceTest.py::TestResource::testStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 268s src/resourceTest.py::TestResource::testPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 268s [gw0] [ 75%] PASSED src/resourceTest.py::TestResource::testPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 268s src/resourceTest.py::TestResource::testStandAloneInPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 268s [gw0] [ 75%] PASSED src/resourceTest.py::TestResource::testStandAloneInPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 268s src/resourceTest.py::TestResource::testBuiltIn <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 268s [gw1] [ 75%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 268s [gw0] [ 75%] PASSED src/resourceTest.py::TestResource::testBuiltIn <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 269s src/resourceTest.py::TestResource::testNonPyStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 269s [gw0] [ 76%] PASSED src/resourceTest.py::TestResource::testNonPyStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 271s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 272s [gw1] [ 76%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 272s [gw0] [ 76%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 273s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithClassMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 273s [gw2] [ 76%] PASSED utils/utilsTest.py::TestUtils::testGetPIDStatus <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 274s utils/utilsTest.py::TestUtils::testGetStatusFailedToilWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 274s [gw1] [ 76%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 274s [gw0] [ 76%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithClassMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 276s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithLambda <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 277s [gw1] [ 76%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 277s [gw0] [ 77%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithLambda <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 278s src/deferredFunctionTest.py::TestDeferredFunction::testBatchSystemCleanupCanHandleWorkerDeaths <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 278s [gw2] [ 77%] PASSED utils/utilsTest.py::TestUtils::testGetStatusFailedToilWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 279s utils/utilsTest.py::TestUtils::testGetStatusFailedCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 281s [gw1] [ 77%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 281s [gw0] [ 77%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testBatchSystemCleanupCanHandleWorkerDeaths <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 281s src/miscTests.py::TestPanic::test_panic_by_hand <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 281s [gw0] [ 77%] PASSED src/miscTests.py::TestPanic::test_panic_by_hand <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 281s src/miscTests.py::TestPanic::test_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 281s [gw0] [ 78%] PASSED src/miscTests.py::TestPanic::test_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 281s src/miscTests.py::TestPanic::test_panic_with_secondary <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 281s [gw0] [ 78%] PASSED src/miscTests.py::TestPanic::test_panic_with_secondary <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 281s src/miscTests.py::TestPanic::test_nested_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 281s [gw0] [ 78%] PASSED src/miscTests.py::TestPanic::test_nested_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 281s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 281s [gw0] [ 78%] 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 281s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 281s [gw0] [ 79%] PASSED batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 281s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_still_running <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 281s [gw0] [ 79%] 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 281s lib/test_conversions.py::ConversionTest::test_convert <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 281s [gw0] [ 79%] PASSED lib/test_conversions.py::ConversionTest::test_convert <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 281s lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 281s [gw0] [ 80%] PASSED lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 281s lib/test_conversions.py::ConversionTest::test_human2bytes <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 281s [gw0] [ 80%] PASSED lib/test_conversions.py::ConversionTest::test_human2bytes <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 281s lib/test_history.py::TestHistory::test_history_submittable_detection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 281s [gw0] [ 80%] PASSED lib/test_history.py::TestHistory::test_history_submittable_detection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 281s lib/test_history.py::TestHistory::test_history_deletion <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 281s [gw0] [ 80%] PASSED lib/test_history.py::TestHistory::test_history_deletion <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 282s lib/test_history.py::TestHistory::test_history_size_limit <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 282s [gw0] [ 81%] PASSED lib/test_history.py::TestHistory::test_history_size_limit <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 282s server/serverTest.py::ToilWESServerBenchTest::test_get_service_info <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 282s [gw0] [ 81%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_get_service_info <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 282s server/serverTest.py::ToilWESServerBenchTest::test_health <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 282s [gw0] [ 81%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_health <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 282s server/serverTest.py::ToilWESServerBenchTest::test_home <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 282s [gw0] [ 81%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_home <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 282s src/busTest.py::TestMessageBus::test_enum_ints_in_file <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 282s [gw0] [ 82%] PASSED src/busTest.py::TestMessageBus::test_enum_ints_in_file <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 282s src/busTest.py::TestMessageBus::test_cross_thread_messaging <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 282s [gw0] [ 82%] PASSED src/busTest.py::TestMessageBus::test_cross_thread_messaging <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 282s src/busTest.py::TestMessageBus::test_restart_without_bus_path <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 283s [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 283s [gw2] [ 82%] PASSED utils/utilsTest.py::TestUtils::testGetStatusFailedCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 284s utils/utilsTest.py::TestUtils::testGetStatusSuccessfulCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 284s [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 284s [gw1] [ 82%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 287s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 287s [gw2] [ 82%] PASSED utils/utilsTest.py::TestUtils::testGetStatusSuccessfulCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 287s utils/utilsTest.py::TestUtils::testPrintJobLog <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 287s [gw1] [ 83%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 291s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 291s [gw0] [ 83%] PASSED src/busTest.py::TestMessageBus::test_restart_without_bus_path <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 292s src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 292s [gw2] [ 83%] PASSED utils/utilsTest.py::TestUtils::testPrintJobLog <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 293s utils/utilsTest.py::TestUtils::testRestartAttribute <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 293s [gw0] [ 84%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 294s src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 294s [gw1] [ 84%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 300s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 300s [gw1] [ 84%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 300s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 300s [gw0] [ 84%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 302s src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 302s [gw1] [ 85%] SUBPASSED[Testing readwrite file permissions 302s [executable: True] 302s [caching: True] 303s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 303s [gw0] [ 85%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 303s src/promisedRequirementTest.py::TestMesosPromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 303s [gw0] [ 85%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 303s src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 303s [gw0] [ 85%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 303s src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 303s [gw0] [ 86%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 305s utils/toilDebugTest.py::TestDebugJob::test_run_job <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 305s [gw1] [ 86%] SUBPASSED[Testing readwrite file permissions 305s [executable: True] 305s [caching: False] 307s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 307s [gw1] [ 86%] SUBPASSED[Testing readwrite file permissions 307s [executable: False] 307s [caching: True] 308s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 308s [gw0] [ 86%] PASSED utils/toilDebugTest.py::TestDebugJob::test_run_job <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 310s utils/toilDebugTest.py::TestDebugJob::test_print_job_info <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 310s [gw1] [ 86%] SUBPASSED[Testing readwrite file permissions 310s [executable: False] 310s [caching: False] 310s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 310s [gw1] [ 86%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 311s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 311s [gw1] [ 86%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 311s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 311s [gw2] [ 86%] PASSED utils/utilsTest.py::TestUtils::testRestartAttribute <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 314s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 314s [gw0] [ 87%] PASSED utils/toilDebugTest.py::TestDebugJob::test_print_job_info <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 314s utils/toilDebugTest.py::TestDebugJob::test_retrieve_task_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 314s [gw0] [ 87%] SKIPPED utils/toilDebugTest.py::TestDebugJob::test_retrieve_task_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 314s __init__.py::toil.test.make_tests <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 314s [gw0] [ 87%] PASSED __init__.py::toil.test.make_tests <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 316s __init__.py::toil.test.timeLimit <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 316s [gw1] [ 88%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 316s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 316s [gw0] [ 88%] PASSED __init__.py::toil.test.timeLimit <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 316s server/serverTest.py::AWSStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 316s [gw0] [ 88%] SKIPPED server/serverTest.py::AWSStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 316s server/serverTest.py::AWSStateStoreTest::test_state_store_paths <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 316s [gw0] [ 88%] SKIPPED server/serverTest.py::AWSStateStoreTest::test_state_store_paths <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 316s src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 316s [gw0] [ 89%] PASSED src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 316s src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 316s [gw0] [ 89%] PASSED src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 317s src/threadingTest.py::TestThreading::testGlobalMutexOrdering <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 317s [gw1] [ 89%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 317s options/options.py::OptionsTest::test_caching_option_priority <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 317s [gw1] [ 89%] PASSED options/options.py::OptionsTest::test_caching_option_priority <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 317s options/options.py::OptionsTest::test_default_caching_slurm <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 317s [gw1] [ 90%] PASSED options/options.py::OptionsTest::test_default_caching_slurm <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 317s 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 317s [gw1] [ 90%] 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 317s jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 317s [gw1] [ 90%] SKIPPED jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 317s lib/test_misc.py::UserNameAvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 317s [gw1] [ 90%] PASSED lib/test_misc.py::UserNameAvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 317s lib/test_misc.py::UserNameUnvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 317s [gw1] [ 91%] PASSED lib/test_misc.py::UserNameUnvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 317s lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 317s [gw1] [ 91%] PASSED lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 317s mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue <- ../../../../usr/lib/python3/dist-packages/toil/test/mesos/MesosDataStructuresTest.py 317s [gw1] [ 91%] PASSED mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue <- ../../../../usr/lib/python3/dist-packages/toil/test/mesos/MesosDataStructuresTest.py 317s provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/provisionerTest.py 317s [gw1] [ 92%] PASSED provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/provisionerTest.py 317s server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 317s [gw1] [ 92%] SKIPPED server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 317s server/serverTest.py::FileStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 317s [gw1] [ 92%] SKIPPED server/serverTest.py::FileStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 317s server/serverTest.py::FileStateStoreURLTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 317s [gw1] [ 92%] SKIPPED server/serverTest.py::FileStateStoreURLTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 319s src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried <- ../../../../usr/lib/python3/dist-packages/toil/test/src/checkpointTest.py 319s [gw2] [ 93%] PASSED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 324s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 324s [gw1] [ 93%] PASSED src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried <- ../../../../usr/lib/python3/dist-packages/toil/test/src/checkpointTest.py 326s src/environmentTest.py::EnvironmentTest::test_environment <- ../../../../usr/lib/python3/dist-packages/toil/test/src/environmentTest.py 326s [gw2] [ 93%] FAILED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 331s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 331s [gw0] [ 93%] PASSED src/threadingTest.py::TestThreading::testGlobalMutexOrdering <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 334s src/threadingTest.py::TestThreading::testLastProcessStanding <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 334s [gw2] [ 94%] FAILED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 339s src/jobServiceTest.py::TestJobService::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 339s [gw1] [ 94%] PASSED src/environmentTest.py::EnvironmentTest::test_environment <- ../../../../usr/lib/python3/dist-packages/toil/test/src/environmentTest.py 344s src/helloWorldTest.py::HelloWorldTest::testHelloWorld <- ../../../../usr/lib/python3/dist-packages/toil/test/src/helloWorldTest.py 344s [gw0] [ 94%] PASSED src/threadingTest.py::TestThreading::testLastProcessStanding <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 344s batchSystems/batch_system_plugin_test.py::BatchSystemPluginTest::test_batchsystem_plugin_installable <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batch_system_plugin_test.py 344s [gw0] [ 94%] 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 346s src/promisesTest.py::ChainedIndexedPromisesTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 346s [gw1] [ 95%] PASSED src/helloWorldTest.py::HelloWorldTest::testHelloWorld <- ../../../../usr/lib/python3/dist-packages/toil/test/src/helloWorldTest.py 346s src/jobServiceTest.py::TestPerfectServicet::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 346s [gw0] [ 95%] PASSED src/promisesTest.py::ChainedIndexedPromisesTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 354s src/resumabilityTest.py::TestResumability::test_chaining <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resumabilityTest.py 354s [gw0] [ 95%] PASSED src/resumabilityTest.py::TestResumability::test_chaining <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resumabilityTest.py 358s src/systemTest.py::TestSystem::testAtomicityOfNonEmptyDirectoryRenames <- ../../../../usr/lib/python3/dist-packages/toil/test/src/systemTest.py 358s [gw2] [ 96%] PASSED src/jobServiceTest.py::TestJobService::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 364s src/promisesTest.py::CachedUnpicklingJobStoreTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 364s [gw2] [ 96%] PASSED src/promisesTest.py::CachedUnpicklingJobStoreTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 366s src/promisesTest.py::PathIndexingPromiseTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 366s [gw2] [ 96%] PASSED src/promisesTest.py::PathIndexingPromiseTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 366s utils/toilKillTest.py::TestToilKillWithAWSJobStore::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 371s [gw2] [ 96%] SKIPPED utils/toilKillTest.py::TestToilKillWithAWSJobStore::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 371s [gw1] [ 97%] PASSED src/jobServiceTest.py::TestPerfectServicet::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 374s src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger <- ../../../../usr/lib/python3/dist-packages/toil/test/src/realtimeLoggerTest.py 374s [gw1] [ 97%] PASSED src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger <- ../../../../usr/lib/python3/dist-packages/toil/test/src/realtimeLoggerTest.py 374s src/workerTest.py::WorkerTests::testNextChainable <- ../../../../usr/lib/python3/dist-packages/toil/test/src/workerTest.py 439s [gw1] [ 97%] PASSED src/workerTest.py::WorkerTests::testNextChainable <- ../../../../usr/lib/python3/dist-packages/toil/test/src/workerTest.py 439s [gw3] [ 97%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 448s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 448s [gw3] [ 98%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 452s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 452s [gw0] [ 98%] PASSED src/systemTest.py::TestSystem::testAtomicityOfNonEmptyDirectoryRenames <- ../../../../usr/lib/python3/dist-packages/toil/test/src/systemTest.py 454s utils/toilDebugTest.py::testFetchJobStoreFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 454s [gw3] [ 98%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 456s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 456s [gw3] [ 98%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 459s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 459s [gw0] [ 99%] PASSED utils/toilDebugTest.py::testFetchJobStoreFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 459s utils/toilKillTest.py::TestToilKill::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 459s [gw0] [ 99%] SKIPPED utils/toilKillTest.py::TestToilKill::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 459s [gw3] [ 99%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 462s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 462s [gw3] [100%] SUBPASSED[Testing readwrite file permissions 462s [executable: True] 462s [caching: True] 464s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 464s [gw3] [100%] SUBPASSED[Testing readwrite file permissions 464s [executable: True] 464s [caching: False] 467s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 467s [gw3] [100%] SUBPASSED[Testing readwrite file permissions 467s [executable: False] 467s [caching: True] 469s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 469s [gw3] [100%] SUBPASSED[Testing readwrite file permissions 469s [executable: False] 469s [caching: False] 469s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 470s [gw3] [100%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 470s 470s ==================================== ERRORS ==================================== 470s _________________ ERROR collecting src/importExportFileTest.py _________________ 470s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py'. 470s Hint: make sure your test modules/packages have valid Python names. 470s Traceback: 470s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 470s mod = import_path( 470s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 470s importlib.import_module(module_name) 470s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 470s return _bootstrap._gcd_import(name[level:], package, level) 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s :1398: in _gcd_import 470s ??? 470s :1371: in _find_and_load 470s ??? 470s :1342: in _find_and_load_unlocked 470s ??? 470s :938: in _load_unlocked 470s ??? 470s :759: in exec_module 470s ??? 470s :491: in _call_with_frames_removed 470s ??? 470s /usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py:30: in 470s from pytest_subtests import SubTests 470s E ModuleNotFoundError: No module named 'pytest_subtests' 470s _________________ ERROR collecting src/jobEncapsulationTest.py _________________ 470s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py'. 470s Hint: make sure your test modules/packages have valid Python names. 470s Traceback: 470s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 470s mod = import_path( 470s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 470s importlib.import_module(module_name) 470s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 470s return _bootstrap._gcd_import(name[level:], package, level) 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s :1398: in _gcd_import 470s ??? 470s :1371: in _find_and_load 470s ??? 470s :1342: in _find_and_load_unlocked 470s ??? 470s :938: in _load_unlocked 470s ??? 470s :759: in exec_module 470s ??? 470s :491: in _call_with_frames_removed 470s ??? 470s /usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py:17: in 470s from toil.test.src.jobTest import fn1Test 470s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 470s from pytest_subtests import SubTests 470s E ModuleNotFoundError: No module named 'pytest_subtests' 470s _______________________ ERROR collecting src/jobTest.py ________________________ 470s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobTest.py'. 470s Hint: make sure your test modules/packages have valid Python names. 470s Traceback: 470s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 470s mod = import_path( 470s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 470s importlib.import_module(module_name) 470s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 470s return _bootstrap._gcd_import(name[level:], package, level) 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s :1398: in _gcd_import 470s ??? 470s :1371: in _find_and_load 470s ??? 470s :1342: in _find_and_load_unlocked 470s ??? 470s :938: in _load_unlocked 470s ??? 470s :759: in exec_module 470s ??? 470s :491: in _call_with_frames_removed 470s ??? 470s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 470s from pytest_subtests import SubTests 470s E ModuleNotFoundError: No module named 'pytest_subtests' 470s =================================== FAILURES =================================== 470s __________________________ TestDocker.testDockerClean __________________________ 470s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 470s toil.start(A) 470s ~~~~~~~~~~^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 470s return self._runMainLoop(rootJobDescription) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 470s ).run() 470s ~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 470s raise FailedJobsException( 470s ...<3 lines>... 470s ) 470s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v3 470s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v3" follows: 470s =========> 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v1 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v1 470s [2026-01-30T23:42:33+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi 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. 470s [2026-01-30T23:42:33+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 470s apiDockerCall( 470s ~~~~~~~~~~~~~^ 470s job, 470s ^^^^ 470s ...<6 lines>... 470s privileged=True, 470s ^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:33+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 470s result: TResult | None = func() 470s ~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 470s lambda: runtest_hook(item=item, **kwds), 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 470s yield 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 470s return result.get_result() 470s ~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 470s raise exc.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 470s res = yield 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 470s item.runtest() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 470s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 470s result = testfunction(**testargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 470s file_stats = test_file.stat() 470s File "/usr/lib/python3.14/pathlib/__init__.py", line 655, in stat 470s return os.stat(self, follow_symlinks=follow_symlinks) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean0/working/test.txt' 470s ----------------------------- Captured stderr call ----------------------------- 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 9acd2965-615d-4f2e-99bf-c2a60a14a795 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean0/jobstore 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil.lib.history] Workflow 9acd2965-615d-4f2e-99bf-c2a60a14a795 is a run of 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:42:33+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-b60k9jsi. 470s [2026-01-30T23:42:33+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v1 470s Exit reason: None 470s [2026-01-30T23:42:33+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v2 470s [2026-01-30T23:42:33+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-b60k9jsi" follows: 470s =========> 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v1 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v1 470s [2026-01-30T23:42:33+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi 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. 470s [2026-01-30T23:42:33+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 470s apiDockerCall( 470s ~~~~~~~~~~~~~^ 470s job, 470s ^^^^ 470s ...<6 lines>... 470s privileged=True, 470s ^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:33+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:42:33+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v2 with ID kind-_testDockerCleanFn/instance-b60k9jsi to 0 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 470s [2026-01-30T23:42:33+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v3 is completely failed 470s [2026-01-30T23:42:33+0000] [Thread-5 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:42:33: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi 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. 470s [2026-01-30T23:42:37+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s [2026-01-30T23:42:37+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 470s [2026-01-30T23:42:37+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v3 470s [2026-01-30T23:42:37+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil.lib.history] Workflow 9acd2965-615d-4f2e-99bf-c2a60a14a795 stopped. Success: False 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean0/jobstore) 470s ------------------------------ Captured log call ------------------------------- 470s INFO  toil.lib.history:history.py:369 Recording workflow creation of 9acd2965-615d-4f2e-99bf-c2a60a14a795 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean0/jobstore 470s INFO  toil.lib.history:history.py:399 Workflow 9acd2965-615d-4f2e-99bf-c2a60a14a795 is a run of 470s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s 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-b60k9jsi. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v1 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v2 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-b60k9jsi" follows: 470s =========> 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v1 470s [2026-01-30T23:42:33+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v1 470s [2026-01-30T23:42:33+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi 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. 470s [2026-01-30T23:42:33+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 470s apiDockerCall( 470s ~~~~~~~~~~~~~^ 470s job, 470s ^^^^ 470s ...<6 lines>... 470s privileged=True, 470s ^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:33+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v2 with ID kind-_testDockerCleanFn/instance-b60k9jsi to 0 470s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 470s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v3 is completely failed 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:42:33: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi 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. 470s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 470s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-b60k9jsi v3 470s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 470s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 470s INFO  toil.lib.history:history.py:530 Workflow 9acd2965-615d-4f2e-99bf-c2a60a14a795 stopped. Success: False 470s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean0/jobstore) 470s _______________________ ToilDocumentationTest.testDocker _______________________ 470s [gw1] linux -- Python 3.14.2 /usr/bin/python3.14 470s Traceback (most recent call last): 470s File "/usr/lib/python3.14/unittest/case.py", line 58, in testPartExecutor 470s yield 470s File "/usr/lib/python3.14/unittest/case.py", line 669, in run 470s self._callTestMethod(testMethod) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ 470s File "/usr/lib/python3.14/unittest/case.py", line 615, in _callTestMethod 470s result = method() 470s File "/usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py", line 161, in testDocker 470s self.checkExitCode("tutorial_docker.py") 470s ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py", line 50, in checkExitCode 470s raise RuntimeError(stderr) 470s RuntimeError: [2026-01-30T23:42:35+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 2fc1ff03-68c0-4019-b651-8a1c66d3aaca in file:/tmp/tmpgtxpsj66tutorial_docker 470s [2026-01-30T23:42:35+0000] [MainThread] [I] [toil.lib.history] Workflow 2fc1ff03-68c0-4019-b651-8a1c66d3aaca is a run of /usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py 470s [2026-01-30T23:42:35+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:35+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 470s [2026-01-30T23:42:35+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:42:36+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmpgtxpsj66tutorial_docker kind-apiDockerCall/instance-jkwrggqq. 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v1 470s Exit reason: None 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v2 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-jkwrggqq" follows: 470s =========> 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v1 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v1) from description 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v1 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq 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. 470s [2026-01-30T23:42:36+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:36+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v2 with ID kind-apiDockerCall/instance-jkwrggqq to 1 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:42:36+0000] [Thread-4 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:42:36: Job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq 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. 470s [2026-01-30T23:42:36+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmpgtxpsj66tutorial_docker kind-apiDockerCall/instance-jkwrggqq. 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v3 470s Exit reason: None 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v5 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-jkwrggqq" follows: 470s =========> 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v4 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v4) from description 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v4 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq 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. 470s [2026-01-30T23:42:36+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:36+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v5 with ID kind-apiDockerCall/instance-jkwrggqq to 0 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.leader] Job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v6 is completely failed 470s [2026-01-30T23:42:36+0000] [Thread-4 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:42:36: Job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq 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. 470s [2026-01-30T23:42:39+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s [2026-01-30T23:42:39+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 470s [2026-01-30T23:42:39+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v6 470s [2026-01-30T23:42:39+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 470s [2026-01-30T23:42:40+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 470s [2026-01-30T23:42:40+0000] [MainThread] [I] [toil.lib.history] Workflow 2fc1ff03-68c0-4019-b651-8a1c66d3aaca stopped. Success: False 470s [2026-01-30T23:42:40+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/tmpgtxpsj66tutorial_docker) 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py", line 20, in 470s toil.start(align) 470s ~~~~~~~~~~^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 470s return self._runMainLoop(rootJobDescription) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 470s ).run() 470s ~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 470s raise FailedJobsException( 470s ...<3 lines>... 470s ) 470s toil.exceptions.FailedJobsException: The job store '/tmp/tmpgtxpsj66tutorial_docker' contains 1 failed jobs: 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v6 470s Log from job "'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v6" follows: 470s =========> 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v4 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v4) from description 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v4 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq 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. 470s [2026-01-30T23:42:36+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:36+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s 470s ---------------------------- Captured stdout setup ----------------------------- 470s 470s 470s [TEST] toil.test.docs.scriptsTest.ToilDocumentationTest:testDocker (Jan 30 2026 15:42:35:642157 PST) 470s 470s 470s _____________________ TestDocker.testDockerClean_CRx_FORGO _____________________ 470s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 470s toil.start(A) 470s ~~~~~~~~~~^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 470s return self._runMainLoop(rootJobDescription) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 470s ).run() 470s ~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 470s raise FailedJobsException( 470s ...<3 lines>... 470s ) 470s 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-vdje64op v3 470s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v3" follows: 470s =========> 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v1 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v1 470s [2026-01-30T23:42:38+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op 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. 470s [2026-01-30T23:42:38+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 470s apiDockerCall( 470s ~~~~~~~~~~~~~^ 470s job, 470s ^^^^ 470s ...<6 lines>... 470s privileged=True, 470s ^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:38+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 470s result: TResult | None = func() 470s ~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 470s lambda: runtest_hook(item=item, **kwds), 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 470s yield 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 470s return result.get_result() 470s ~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 470s raise exc.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 470s res = yield 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 470s item.runtest() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 470s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 470s result = testfunction(**testargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 133, in testDockerClean_CRx_FORGO 470s self.testDockerClean( 470s ~~~~~~~~~~~~~~~~~~~~^ 470s tmp_path, caching=False, detached=False, rm=True, deferParam=FORGO 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 470s file_stats = test_file.stat() 470s File "/usr/lib/python3.14/pathlib/__init__.py", line 655, in stat 470s return os.stat(self, follow_symlinks=follow_symlinks) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_FORGO0/working/test.txt' 470s ----------------------------- Captured stderr call ----------------------------- 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 710f5371-2526-4b1a-85be-77e6ecef89ff in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_FORGO0/jobstore 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil.lib.history] Workflow 710f5371-2526-4b1a-85be-77e6ecef89ff is a run of 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:42:38+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-vdje64op. 470s [2026-01-30T23:42:38+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v1 470s Exit reason: None 470s [2026-01-30T23:42:38+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v2 470s [2026-01-30T23:42:38+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-vdje64op" follows: 470s =========> 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v1 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v1 470s [2026-01-30T23:42:38+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op 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. 470s [2026-01-30T23:42:38+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 470s apiDockerCall( 470s ~~~~~~~~~~~~~^ 470s job, 470s ^^^^ 470s ...<6 lines>... 470s privileged=True, 470s ^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:38+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:42:38+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v2 with ID kind-_testDockerCleanFn/instance-vdje64op to 0 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 470s [2026-01-30T23:42:38+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v3 is completely failed 470s [2026-01-30T23:42:38+0000] [Thread-9 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:42:38: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op 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. 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v3 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.lib.history] Workflow 710f5371-2526-4b1a-85be-77e6ecef89ff stopped. Success: False 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_FORGO0/jobstore) 470s ------------------------------ Captured log call ------------------------------- 470s INFO  toil.lib.history:history.py:369 Recording workflow creation of 710f5371-2526-4b1a-85be-77e6ecef89ff in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_FORGO0/jobstore 470s INFO  toil.lib.history:history.py:399 Workflow 710f5371-2526-4b1a-85be-77e6ecef89ff is a run of 470s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s 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-vdje64op. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v1 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v2 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-vdje64op" follows: 470s =========> 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v1 470s [2026-01-30T23:42:38+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v1 470s [2026-01-30T23:42:38+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op 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. 470s [2026-01-30T23:42:38+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 470s apiDockerCall( 470s ~~~~~~~~~~~~~^ 470s job, 470s ^^^^ 470s ...<6 lines>... 470s privileged=True, 470s ^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:38+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v2 with ID kind-_testDockerCleanFn/instance-vdje64op to 0 470s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 470s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v3 is completely failed 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:42:38: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op 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. 470s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 470s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-vdje64op v3 470s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 470s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 470s INFO  toil.lib.history:history.py:530 Workflow 710f5371-2526-4b1a-85be-77e6ecef89ff stopped. Success: False 470s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_FORGO0/jobstore) 470s _____________________ TestDocker.testDockerClean_CRx_STOP ______________________ 470s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 470s toil.start(A) 470s ~~~~~~~~~~^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 470s return self._runMainLoop(rootJobDescription) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 470s ).run() 470s ~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 470s raise FailedJobsException( 470s ...<3 lines>... 470s ) 470s 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-x5nhwhi9 v3 470s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v3" follows: 470s =========> 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v1 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v1 470s [2026-01-30T23:42:42+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 470s apiDockerCall( 470s ~~~~~~~~~~~~~^ 470s job, 470s ^^^^ 470s ...<6 lines>... 470s privileged=True, 470s ^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:42+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 470s result: TResult | None = func() 470s ~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 470s lambda: runtest_hook(item=item, **kwds), 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 470s yield 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 470s return result.get_result() 470s ~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 470s raise exc.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 470s res = yield 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 470s item.runtest() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 470s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 470s result = testfunction(**testargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 138, in testDockerClean_CRx_STOP 470s self.testDockerClean( 470s ~~~~~~~~~~~~~~~~~~~~^ 470s tmp_path, caching=False, detached=False, rm=True, deferParam=STOP 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 470s file_stats = test_file.stat() 470s File "/usr/lib/python3.14/pathlib/__init__.py", line 655, in stat 470s return os.stat(self, follow_symlinks=follow_symlinks) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_STOP0/working/test.txt' 470s ----------------------------- Captured stderr call ----------------------------- 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of b2294b2c-34fd-45df-baa6-3f654a033beb in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_STOP0/jobstore 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.lib.history] Workflow b2294b2c-34fd-45df-baa6-3f654a033beb is a run of 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:42:42+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-x5nhwhi9. 470s [2026-01-30T23:42:42+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v1 470s Exit reason: None 470s [2026-01-30T23:42:42+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v2 470s [2026-01-30T23:42:42+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-x5nhwhi9" follows: 470s =========> 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v1 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v1 470s [2026-01-30T23:42:42+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 470s apiDockerCall( 470s ~~~~~~~~~~~~~^ 470s job, 470s ^^^^ 470s ...<6 lines>... 470s privileged=True, 470s ^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:42+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:42:42+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v2 with ID kind-_testDockerCleanFn/instance-x5nhwhi9 to 0 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 470s [2026-01-30T23:42:42+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v3 is completely failed 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v3 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.lib.history] Workflow b2294b2c-34fd-45df-baa6-3f654a033beb stopped. Success: False 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_STOP0/jobstore) 470s ------------------------------ Captured log call ------------------------------- 470s INFO  toil.lib.history:history.py:369 Recording workflow creation of b2294b2c-34fd-45df-baa6-3f654a033beb in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_STOP0/jobstore 470s INFO  toil.lib.history:history.py:399 Workflow b2294b2c-34fd-45df-baa6-3f654a033beb is a run of 470s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s 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-x5nhwhi9. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v1 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v2 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-x5nhwhi9" follows: 470s =========> 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v1 470s [2026-01-30T23:42:42+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v1 470s [2026-01-30T23:42:42+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 470s apiDockerCall( 470s ~~~~~~~~~~~~~^ 470s job, 470s ^^^^ 470s ...<6 lines>... 470s privileged=True, 470s ^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:42+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v2 with ID kind-_testDockerCleanFn/instance-x5nhwhi9 to 0 470s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 470s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v3 is completely failed 470s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 470s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-x5nhwhi9 v3 470s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 470s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 470s INFO  toil.lib.history:history.py:530 Workflow b2294b2c-34fd-45df-baa6-3f654a033beb stopped. Success: False 470s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_STOP0/jobstore) 470s ______________________ TestDocker.testDockerClean_CRx_RM _______________________ 470s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 470s toil.start(A) 470s ~~~~~~~~~~^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 470s return self._runMainLoop(rootJobDescription) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 470s ).run() 470s ~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 470s raise FailedJobsException( 470s ...<3 lines>... 470s ) 470s 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-a4g3or20 v3 470s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v3" follows: 470s =========> 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v1 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v1 470s [2026-01-30T23:42:46+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 470s apiDockerCall( 470s ~~~~~~~~~~~~~^ 470s job, 470s ^^^^ 470s ...<6 lines>... 470s privileged=True, 470s ^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:46+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 470s result: TResult | None = func() 470s ~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 470s lambda: runtest_hook(item=item, **kwds), 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 470s yield 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 470s return result.get_result() 470s ~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 470s raise exc.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 470s res = yield 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 470s item.runtest() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 470s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 470s result = testfunction(**testargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 143, in testDockerClean_CRx_RM 470s self.testDockerClean( 470s ~~~~~~~~~~~~~~~~~~~~^ 470s tmp_path, caching=False, detached=False, rm=True, deferParam=RM 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 470s file_stats = test_file.stat() 470s File "/usr/lib/python3.14/pathlib/__init__.py", line 655, in stat 470s return os.stat(self, follow_symlinks=follow_symlinks) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_RM0/working/test.txt' 470s ----------------------------- Captured stderr call ----------------------------- 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 4ce67876-8b5a-4cee-9fd0-083dd113edc7 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_RM0/jobstore 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.lib.history] Workflow 4ce67876-8b5a-4cee-9fd0-083dd113edc7 is a run of 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:42:46+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-a4g3or20. 470s [2026-01-30T23:42:46+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v1 470s Exit reason: None 470s [2026-01-30T23:42:46+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v2 470s [2026-01-30T23:42:46+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-a4g3or20" follows: 470s =========> 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v1 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v1 470s [2026-01-30T23:42:46+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 470s apiDockerCall( 470s ~~~~~~~~~~~~~^ 470s job, 470s ^^^^ 470s ...<6 lines>... 470s privileged=True, 470s ^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:46+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:42:46+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v2 with ID kind-_testDockerCleanFn/instance-a4g3or20 to 0 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 470s [2026-01-30T23:42:46+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v3 is completely failed 470s [2026-01-30T23:42:50+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s [2026-01-30T23:42:50+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 470s [2026-01-30T23:42:50+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v3 470s [2026-01-30T23:42:50+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 470s [2026-01-30T23:42:50+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 470s [2026-01-30T23:42:50+0000] [MainThread] [I] [toil.lib.history] Workflow 4ce67876-8b5a-4cee-9fd0-083dd113edc7 stopped. Success: False 470s [2026-01-30T23:42:50+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_RM0/jobstore) 470s ------------------------------ Captured log call ------------------------------- 470s INFO  toil.lib.history:history.py:369 Recording workflow creation of 4ce67876-8b5a-4cee-9fd0-083dd113edc7 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_RM0/jobstore 470s INFO  toil.lib.history:history.py:399 Workflow 4ce67876-8b5a-4cee-9fd0-083dd113edc7 is a run of 470s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s 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-a4g3or20. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v1 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v2 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-a4g3or20" follows: 470s =========> 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v1 470s [2026-01-30T23:42:46+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v1 470s [2026-01-30T23:42:46+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 470s apiDockerCall( 470s ~~~~~~~~~~~~~^ 470s job, 470s ^^^^ 470s ...<6 lines>... 470s privileged=True, 470s ^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:46+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v2 with ID kind-_testDockerCleanFn/instance-a4g3or20 to 0 470s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 470s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v3 is completely failed 470s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 470s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-a4g3or20 v3 470s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 470s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 470s INFO  toil.lib.history:history.py:530 Workflow 4ce67876-8b5a-4cee-9fd0-083dd113edc7 stopped. Success: False 470s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerClean_CRx_RM0/jobstore) 470s ________________________ TestDocker.testDockerPipeChain ________________________ 470s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 470s result: TResult | None = func() 470s ~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 470s lambda: runtest_hook(item=item, **kwds), 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 470s yield 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 470s return result.get_result() 470s ~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 470s raise exc.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 470s res = yield 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 470s item.runtest() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 470s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 470s result = testfunction(**testargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 310, in testDockerPipeChain 470s rv = Job.Runner.startToil(A, options) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 470s return toil.start(job) 470s ~~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 470s return self._runMainLoop(rootJobDescription) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 470s ).run() 470s ~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 470s raise FailedJobsException( 470s ...<3 lines>... 470s ) 470s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v6 470s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v6" follows: 470s =========> 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v4 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v4 470s [2026-01-30T23:42:51+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ 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. 470s [2026-01-30T23:42:51+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 470s return apiDockerCall( 470s job, 470s ...<2 lines>... 470s privileged=True, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:51+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s ----------------------------- Captured stderr call ----------------------------- 470s [2026-01-30T23:42:50+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 83cee3ef-24a7-47f0-b6e2-ec72ccc89e63 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChain0/jobstore 470s [2026-01-30T23:42:50+0000] [MainThread] [I] [toil.lib.history] Workflow 83cee3ef-24a7-47f0-b6e2-ec72ccc89e63 is a run of 470s [2026-01-30T23:42:50+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:50+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 470s [2026-01-30T23:42:50+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:42:51+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-8mvo8au_. 470s [2026-01-30T23:42:51+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v1 470s Exit reason: None 470s [2026-01-30T23:42:51+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v2 470s [2026-01-30T23:42:51+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-8mvo8au_" follows: 470s =========> 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v1 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v1 470s [2026-01-30T23:42:51+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ 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. 470s [2026-01-30T23:42:51+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 470s return apiDockerCall( 470s job, 470s ...<2 lines>... 470s privileged=True, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:51+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:42:51+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v2 with ID kind-_testDockerPipeChainFn/instance-8mvo8au_ to 1 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:42:51+0000] [Thread-21 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:42:51: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ 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. 470s [2026-01-30T23:42:51+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-8mvo8au_. 470s [2026-01-30T23:42:51+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v3 470s Exit reason: None 470s [2026-01-30T23:42:51+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v5 470s [2026-01-30T23:42:51+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-8mvo8au_" follows: 470s =========> 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v4 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v4 470s [2026-01-30T23:42:51+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ 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. 470s [2026-01-30T23:42:51+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 470s return apiDockerCall( 470s job, 470s ...<2 lines>... 470s privileged=True, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:51+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:42:51+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v5 with ID kind-_testDockerPipeChainFn/instance-8mvo8au_ to 0 470s [2026-01-30T23:42:51+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v6 is completely failed 470s [2026-01-30T23:42:51+0000] [Thread-21 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:42:51: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ 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. 470s [2026-01-30T23:42:54+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s [2026-01-30T23:42:54+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 470s [2026-01-30T23:42:54+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v6 470s [2026-01-30T23:42:54+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 470s [2026-01-30T23:42:55+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 470s [2026-01-30T23:42:55+0000] [MainThread] [I] [toil.lib.history] Workflow 83cee3ef-24a7-47f0-b6e2-ec72ccc89e63 stopped. Success: False 470s [2026-01-30T23:42:55+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChain0/jobstore) 470s ------------------------------ Captured log call ------------------------------- 470s INFO  toil.lib.history:history.py:369 Recording workflow creation of 83cee3ef-24a7-47f0-b6e2-ec72ccc89e63 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChain0/jobstore 470s INFO  toil.lib.history:history.py:399 Workflow 83cee3ef-24a7-47f0-b6e2-ec72ccc89e63 is a run of 470s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s 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-8mvo8au_. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v1 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v2 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-8mvo8au_" follows: 470s =========> 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v1 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v1 470s [2026-01-30T23:42:51+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ 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. 470s [2026-01-30T23:42:51+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 470s return apiDockerCall( 470s job, 470s ...<2 lines>... 470s privileged=True, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:51+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v2 with ID kind-_testDockerPipeChainFn/instance-8mvo8au_ to 1 470s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:42:51: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ 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. 470s 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-8mvo8au_. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v3 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v5 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-8mvo8au_" follows: 470s =========> 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v4 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v4 470s [2026-01-30T23:42:51+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ 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. 470s [2026-01-30T23:42:51+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 470s return apiDockerCall( 470s job, 470s ...<2 lines>... 470s privileged=True, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:51+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v5 with ID kind-_testDockerPipeChainFn/instance-8mvo8au_ to 0 470s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v6 is completely failed 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:42:51: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ 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. 470s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 470s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v6 470s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 470s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 470s INFO  toil.lib.history:history.py:530 Workflow 83cee3ef-24a7-47f0-b6e2-ec72ccc89e63 stopped. Success: False 470s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChain0/jobstore) 470s _________________ TestDocker.testDockerPipeChainErrorDetection _________________ 470s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 470s result: TResult | None = func() 470s ~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 470s lambda: runtest_hook(item=item, **kwds), 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 470s yield 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 470s return result.get_result() 470s ~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 470s raise exc.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 470s res = yield 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 470s item.runtest() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 470s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 470s result = testfunction(**testargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 332, in testDockerPipeChainErrorDetection 470s rv = Job.Runner.startToil(A, options) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 470s return toil.start(job) 470s ~~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 470s return self._runMainLoop(rootJobDescription) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 470s ).run() 470s ~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 470s raise FailedJobsException( 470s ...<3 lines>... 470s ) 470s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChainErrorDetect0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v6 470s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v6" follows: 470s =========> 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v4 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v4 470s [2026-01-30T23:42:56+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars 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. 470s [2026-01-30T23:42:56+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 470s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 470s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:56+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s ----------------------------- Captured stderr call ----------------------------- 470s [2026-01-30T23:42:55+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 80f237dd-f2a2-458a-a090-ccb6d8847796 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChainErrorDetect0/jobstore 470s [2026-01-30T23:42:55+0000] [MainThread] [I] [toil.lib.history] Workflow 80f237dd-f2a2-458a-a090-ccb6d8847796 is a run of 470s [2026-01-30T23:42:55+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:55+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 470s [2026-01-30T23:42:55+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:42:56+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-vvxmcars. 470s [2026-01-30T23:42:56+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v1 470s Exit reason: None 470s [2026-01-30T23:42:56+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v2 470s [2026-01-30T23:42:56+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-vvxmcars" follows: 470s =========> 470s [2026-01-30T23:42:55+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:55+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:55+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v1 470s [2026-01-30T23:42:55+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v1 470s [2026-01-30T23:42:55+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars 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. 470s [2026-01-30T23:42:55+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 470s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 470s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:55+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:42:56+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v2 with ID kind-_testDockerPipeChainErrorFn/instance-vvxmcars to 1 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:42:56+0000] [Thread-25 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:42:56: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars 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. 470s [2026-01-30T23:42:56+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-vvxmcars. 470s [2026-01-30T23:42:56+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v3 470s Exit reason: None 470s [2026-01-30T23:42:56+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v5 470s [2026-01-30T23:42:56+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-vvxmcars" follows: 470s =========> 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v4 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v4 470s [2026-01-30T23:42:56+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars 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. 470s [2026-01-30T23:42:56+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 470s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 470s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:56+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:42:56+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v5 with ID kind-_testDockerPipeChainErrorFn/instance-vvxmcars to 0 470s [2026-01-30T23:42:56+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v6 is completely failed 470s [2026-01-30T23:42:56+0000] [Thread-25 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:42:56: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars 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. 470s [2026-01-30T23:42:59+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s [2026-01-30T23:42:59+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 470s [2026-01-30T23:42:59+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v6 470s [2026-01-30T23:42:59+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.lib.history] Workflow 80f237dd-f2a2-458a-a090-ccb6d8847796 stopped. Success: False 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChainErrorDetect0/jobstore) 470s ------------------------------ Captured log call ------------------------------- 470s INFO  toil.lib.history:history.py:369 Recording workflow creation of 80f237dd-f2a2-458a-a090-ccb6d8847796 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChainErrorDetect0/jobstore 470s INFO  toil.lib.history:history.py:399 Workflow 80f237dd-f2a2-458a-a090-ccb6d8847796 is a run of 470s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s 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-vvxmcars. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v1 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v2 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-vvxmcars" follows: 470s =========> 470s [2026-01-30T23:42:55+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:55+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:55+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v1 470s [2026-01-30T23:42:55+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v1 470s [2026-01-30T23:42:55+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars 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. 470s [2026-01-30T23:42:55+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 470s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 470s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:55+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v2 with ID kind-_testDockerPipeChainErrorFn/instance-vvxmcars to 1 470s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:42:56: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars 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. 470s 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-vvxmcars. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v3 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v5 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-vvxmcars" follows: 470s =========> 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v4 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v4 470s [2026-01-30T23:42:56+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars 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. 470s [2026-01-30T23:42:56+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 470s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 470s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:56+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v5 with ID kind-_testDockerPipeChainErrorFn/instance-vvxmcars to 0 470s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v6 is completely failed 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:42:56: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars 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. 470s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 470s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v6 470s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 470s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 470s INFO  toil.lib.history:history.py:530 Workflow 80f237dd-f2a2-458a-a090-ccb6d8847796 stopped. Success: False 470s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerPipeChainErrorDetect0/jobstore) 470s _____________________ TestDocker.testNonCachingDockerChain _____________________ 470s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 470s result: TResult | None = func() 470s ~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 470s lambda: runtest_hook(item=item, **kwds), 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 470s yield 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 470s return result.get_result() 470s ~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 470s raise exc.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 470s res = yield 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 470s item.runtest() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 470s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 470s result = testfunction(**testargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 336, in testNonCachingDockerChain 470s self.testDockerPipeChain(tmp_path, caching=True) 470s ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 310, in testDockerPipeChain 470s rv = Job.Runner.startToil(A, options) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 470s return toil.start(job) 470s ~~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 470s return self._runMainLoop(rootJobDescription) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 470s ).run() 470s ~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 470s raise FailedJobsException( 470s ...<3 lines>... 470s ) 470s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v6 470s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v6" follows: 470s =========> 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v4 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v4 470s [2026-01-30T23:43:00+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y 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. 470s [2026-01-30T23:43:00+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 470s return apiDockerCall( 470s job, 470s ...<2 lines>... 470s privileged=True, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:00+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s ----------------------------- Captured stderr call ----------------------------- 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of f4271319-a1ac-421b-86ab-3a7702bf6e37 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChain0/jobstore 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.lib.history] Workflow f4271319-a1ac-421b-86ab-3a7702bf6e37 is a run of 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:43:00+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-blbzi76y. 470s [2026-01-30T23:43:00+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v1 470s Exit reason: None 470s [2026-01-30T23:43:00+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v2 470s [2026-01-30T23:43:00+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-blbzi76y" follows: 470s =========> 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v1 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v1 470s [2026-01-30T23:43:00+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 470s return apiDockerCall( 470s job, 470s ...<2 lines>... 470s privileged=True, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:00+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:43:00+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v2 with ID kind-_testDockerPipeChainFn/instance-blbzi76y to 1 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:43:01+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-blbzi76y. 470s [2026-01-30T23:43:01+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v3 470s Exit reason: None 470s [2026-01-30T23:43:01+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v5 470s [2026-01-30T23:43:01+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-blbzi76y" follows: 470s =========> 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v4 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v4 470s [2026-01-30T23:43:00+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y 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. 470s [2026-01-30T23:43:00+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 470s return apiDockerCall( 470s job, 470s ...<2 lines>... 470s privileged=True, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:00+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:43:01+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v5 with ID kind-_testDockerPipeChainFn/instance-blbzi76y to 0 470s [2026-01-30T23:43:01+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v6 is completely failed 470s [2026-01-30T23:43:01+0000] [Thread-29 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:43:01: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y 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. 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v6 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.lib.history] Workflow f4271319-a1ac-421b-86ab-3a7702bf6e37 stopped. Success: False 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChain0/jobstore) 470s ------------------------------ Captured log call ------------------------------- 470s INFO  toil.lib.history:history.py:369 Recording workflow creation of f4271319-a1ac-421b-86ab-3a7702bf6e37 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChain0/jobstore 470s INFO  toil.lib.history:history.py:399 Workflow f4271319-a1ac-421b-86ab-3a7702bf6e37 is a run of 470s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s 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-blbzi76y. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v1 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v2 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-blbzi76y" follows: 470s =========> 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v1 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v1 470s [2026-01-30T23:43:00+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 470s return apiDockerCall( 470s job, 470s ...<2 lines>... 470s privileged=True, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:00+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v2 with ID kind-_testDockerPipeChainFn/instance-blbzi76y to 1 470s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s 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-blbzi76y. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v3 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v5 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-blbzi76y" follows: 470s =========> 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v4 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v4 470s [2026-01-30T23:43:00+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y 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. 470s [2026-01-30T23:43:00+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 470s return apiDockerCall( 470s job, 470s ...<2 lines>... 470s privileged=True, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:00+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v5 with ID kind-_testDockerPipeChainFn/instance-blbzi76y to 0 470s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v6 is completely failed 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:43:01: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y 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. 470s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 470s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v6 470s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 470s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 470s INFO  toil.lib.history:history.py:530 Workflow f4271319-a1ac-421b-86ab-3a7702bf6e37 stopped. Success: False 470s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChain0/jobstore) 470s ______________ TestDocker.testNonCachingDockerChainErrorDetection ______________ 470s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 470s result: TResult | None = func() 470s ~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 470s lambda: runtest_hook(item=item, **kwds), 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 470s yield 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 470s return result.get_result() 470s ~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 470s raise exc.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 470s res = yield 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 470s item.runtest() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 470s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 470s result = testfunction(**testargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 339, in testNonCachingDockerChainErrorDetection 470s self.testDockerPipeChainErrorDetection(tmp_path, caching=True) 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 332, in testDockerPipeChainErrorDetection 470s rv = Job.Runner.startToil(A, options) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 470s return toil.start(job) 470s ~~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 470s return self._runMainLoop(rootJobDescription) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 470s ).run() 470s ~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 470s raise FailedJobsException( 470s ...<3 lines>... 470s ) 470s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChainError0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v6 470s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v6" follows: 470s =========> 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v4 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v4 470s [2026-01-30T23:43:05+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz 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. 470s [2026-01-30T23:43:05+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 470s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 470s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:05+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s ----------------------------- Captured stderr call ----------------------------- 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 1373a656-5a2e-4c00-ab89-b0b3fdc996ed in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChainError0/jobstore 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.lib.history] Workflow 1373a656-5a2e-4c00-ab89-b0b3fdc996ed is a run of 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:43:04+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-pfq3h7nz. 470s [2026-01-30T23:43:04+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v1 470s Exit reason: None 470s [2026-01-30T23:43:04+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v2 470s [2026-01-30T23:43:04+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz" follows: 470s =========> 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v1 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v1 470s [2026-01-30T23:43:04+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz 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. 470s [2026-01-30T23:43:04+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 470s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 470s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:04+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:43:04+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v2 with ID kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz to 1 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:43:04+0000] [Thread-33 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:43:04: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz 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. 470s [2026-01-30T23:43:05+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-pfq3h7nz. 470s [2026-01-30T23:43:05+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v3 470s Exit reason: None 470s [2026-01-30T23:43:05+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v5 470s [2026-01-30T23:43:05+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz" follows: 470s =========> 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v4 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v4 470s [2026-01-30T23:43:05+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz 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. 470s [2026-01-30T23:43:05+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 470s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 470s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:05+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:43:05+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v5 with ID kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz to 0 470s [2026-01-30T23:43:05+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v6 is completely failed 470s [2026-01-30T23:43:05+0000] [Thread-33 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:43:05: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz 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. 470s [2026-01-30T23:43:08+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s [2026-01-30T23:43:08+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 470s [2026-01-30T23:43:08+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v6 470s [2026-01-30T23:43:08+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 470s [2026-01-30T23:43:08+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 470s [2026-01-30T23:43:08+0000] [MainThread] [I] [toil.lib.history] Workflow 1373a656-5a2e-4c00-ab89-b0b3fdc996ed stopped. Success: False 470s [2026-01-30T23:43:08+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChainError0/jobstore) 470s ------------------------------ Captured log call ------------------------------- 470s INFO  toil.lib.history:history.py:369 Recording workflow creation of 1373a656-5a2e-4c00-ab89-b0b3fdc996ed in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChainError0/jobstore 470s INFO  toil.lib.history:history.py:399 Workflow 1373a656-5a2e-4c00-ab89-b0b3fdc996ed is a run of 470s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s 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-pfq3h7nz. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v1 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v2 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz" follows: 470s =========> 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v1 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v1 470s [2026-01-30T23:43:04+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz 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. 470s [2026-01-30T23:43:04+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 470s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 470s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:04+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v2 with ID kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz to 1 470s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:43:04: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz 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. 470s 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-pfq3h7nz. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v3 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v5 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz" follows: 470s =========> 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v4 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v4 470s [2026-01-30T23:43:05+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz 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. 470s [2026-01-30T23:43:05+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 470s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 470s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:05+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v5 with ID kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz to 0 470s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v6 is completely failed 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:43:05: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz 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. 470s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 470s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v6 470s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 470s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 470s INFO  toil.lib.history:history.py:530 Workflow 1373a656-5a2e-4c00-ab89-b0b3fdc996ed stopped. Success: False 470s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testNonCachingDockerChainError0/jobstore) 470s __________________________ TestDocker.testDockerLogs ___________________________ 470s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 470s result: TResult | None = func() 470s ~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 470s lambda: runtest_hook(item=item, **kwds), 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 470s yield 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 470s return result.get_result() 470s ~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 470s raise exc.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 470s res = yield 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 470s item.runtest() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 470s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 470s result = testfunction(**testargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 470s rv = Job.Runner.startToil(A, options) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 470s return toil.start(job) 470s ~~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 470s return self._runMainLoop(rootJobDescription) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 470s ).run() 470s ~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 470s raise FailedJobsException( 470s ...<3 lines>... 470s ) 470s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v6 470s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v6" follows: 470s =========> 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v4 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v4 470s [2026-01-30T23:43:11+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 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. 470s [2026-01-30T23:43:11+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:11+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s ----------------------------- Captured stderr call ----------------------------- 470s [2026-01-30T23:43:09+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 6c4cbc1a-2d20-4dcc-8a3e-b778d4f92984 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs0/jobstore 470s [2026-01-30T23:43:09+0000] [MainThread] [I] [toil.lib.history] Workflow 6c4cbc1a-2d20-4dcc-8a3e-b778d4f92984 is a run of 470s [2026-01-30T23:43:09+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:09+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 470s [2026-01-30T23:43:09+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:43:11+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-iytpr4c6. 470s [2026-01-30T23:43:11+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v1 470s Exit reason: None 470s [2026-01-30T23:43:11+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v2 470s [2026-01-30T23:43:11+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-iytpr4c6" follows: 470s =========> 470s [2026-01-30T23:43:10+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:10+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:10+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v1 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v1 470s [2026-01-30T23:43:11+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 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. 470s [2026-01-30T23:43:11+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:11+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:43:11+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v2 with ID kind-_testDockerLogsFn/instance-iytpr4c6 to 1 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:43:11+0000] [Thread-37 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:43:11: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 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. 470s [2026-01-30T23:43:11+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-iytpr4c6. 470s [2026-01-30T23:43:11+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v3 470s Exit reason: None 470s [2026-01-30T23:43:11+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v5 470s [2026-01-30T23:43:11+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-iytpr4c6" follows: 470s =========> 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v4 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v4 470s [2026-01-30T23:43:11+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 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. 470s [2026-01-30T23:43:11+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:11+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:43:11+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v5 with ID kind-_testDockerLogsFn/instance-iytpr4c6 to 0 470s [2026-01-30T23:43:11+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v6 is completely failed 470s [2026-01-30T23:43:12+0000] [Thread-37 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:43:12: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 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. 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v6 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil.lib.history] Workflow 6c4cbc1a-2d20-4dcc-8a3e-b778d4f92984 stopped. Success: False 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs0/jobstore) 470s ------------------------------ Captured log call ------------------------------- 470s INFO  toil.lib.history:history.py:369 Recording workflow creation of 6c4cbc1a-2d20-4dcc-8a3e-b778d4f92984 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs0/jobstore 470s INFO  toil.lib.history:history.py:399 Workflow 6c4cbc1a-2d20-4dcc-8a3e-b778d4f92984 is a run of 470s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s 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-iytpr4c6. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v1 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v2 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-iytpr4c6" follows: 470s =========> 470s [2026-01-30T23:43:10+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:10+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:10+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v1 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v1 470s [2026-01-30T23:43:11+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 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. 470s [2026-01-30T23:43:11+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:11+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v2 with ID kind-_testDockerLogsFn/instance-iytpr4c6 to 1 470s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:43:11: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 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. 470s 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-iytpr4c6. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v3 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v5 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-iytpr4c6" follows: 470s =========> 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v4 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v4 470s [2026-01-30T23:43:11+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 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. 470s [2026-01-30T23:43:11+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:11+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v5 with ID kind-_testDockerLogsFn/instance-iytpr4c6 to 0 470s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v6 is completely failed 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:43:12: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 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. 470s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 470s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v6 470s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 470s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 470s INFO  toil.lib.history:history.py:530 Workflow 6c4cbc1a-2d20-4dcc-8a3e-b778d4f92984 stopped. Success: False 470s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs0/jobstore) 470s _______________________ TestDocker.testDockerLogs_Stream _______________________ 470s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 470s result: TResult | None = func() 470s ~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 470s lambda: runtest_hook(item=item, **kwds), 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 470s yield 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 470s return result.get_result() 470s ~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 470s raise exc.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 470s res = yield 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 470s item.runtest() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 470s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 470s result = testfunction(**testargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 366, in testDockerLogs_Stream 470s self.testDockerLogs(tmp_path, stream=True, demux=False) 470s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 470s rv = Job.Runner.startToil(A, options) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 470s return toil.start(job) 470s ~~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 470s return self._runMainLoop(rootJobDescription) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 470s ).run() 470s ~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 470s raise FailedJobsException( 470s ...<3 lines>... 470s ) 470s 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-3rqvtl5u v6 470s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v6" follows: 470s =========> 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v4 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v4 470s [2026-01-30T23:43:17+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u 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. 470s [2026-01-30T23:43:17+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:17+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s ----------------------------- Captured stderr call ----------------------------- 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of e52e348c-3421-46d2-a0dc-554769b25122 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Stream0/jobstore 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil.lib.history] Workflow e52e348c-3421-46d2-a0dc-554769b25122 is a run of 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:43:17+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-3rqvtl5u. 470s [2026-01-30T23:43:17+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v1 470s Exit reason: None 470s [2026-01-30T23:43:17+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v2 470s [2026-01-30T23:43:17+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-3rqvtl5u" follows: 470s =========> 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v1 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v1 470s [2026-01-30T23:43:16+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u 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. 470s [2026-01-30T23:43:17+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:17+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:43:17+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v2 with ID kind-_testDockerLogsFn/instance-3rqvtl5u to 1 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:43:17+0000] [Thread-41 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:43:17: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u 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. 470s [2026-01-30T23:43:17+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-3rqvtl5u. 470s [2026-01-30T23:43:17+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v3 470s Exit reason: None 470s [2026-01-30T23:43:17+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v5 470s [2026-01-30T23:43:17+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-3rqvtl5u" follows: 470s =========> 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v4 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v4 470s [2026-01-30T23:43:17+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u 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. 470s [2026-01-30T23:43:17+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:17+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:43:17+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v5 with ID kind-_testDockerLogsFn/instance-3rqvtl5u to 0 470s [2026-01-30T23:43:17+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v6 is completely failed 470s [2026-01-30T23:43:17+0000] [Thread-41 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:43:17: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u 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. 470s [2026-01-30T23:43:20+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s [2026-01-30T23:43:20+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 470s [2026-01-30T23:43:20+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v6 470s [2026-01-30T23:43:20+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.lib.history] Workflow e52e348c-3421-46d2-a0dc-554769b25122 stopped. Success: False 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Stream0/jobstore) 470s ------------------------------ Captured log call ------------------------------- 470s INFO  toil.lib.history:history.py:369 Recording workflow creation of e52e348c-3421-46d2-a0dc-554769b25122 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Stream0/jobstore 470s INFO  toil.lib.history:history.py:399 Workflow e52e348c-3421-46d2-a0dc-554769b25122 is a run of 470s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s 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-3rqvtl5u. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v1 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v2 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-3rqvtl5u" follows: 470s =========> 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v1 470s [2026-01-30T23:43:16+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v1 470s [2026-01-30T23:43:16+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u 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. 470s [2026-01-30T23:43:17+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:17+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v2 with ID kind-_testDockerLogsFn/instance-3rqvtl5u to 1 470s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:43:17: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u 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. 470s 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-3rqvtl5u. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v3 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v5 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-3rqvtl5u" follows: 470s =========> 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v4 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v4 470s [2026-01-30T23:43:17+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u 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. 470s [2026-01-30T23:43:17+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:17+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v5 with ID kind-_testDockerLogsFn/instance-3rqvtl5u to 0 470s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v6 is completely failed 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:43:17: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u 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. 470s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 470s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v6 470s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 470s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 470s INFO  toil.lib.history:history.py:530 Workflow e52e348c-3421-46d2-a0dc-554769b25122 stopped. Success: False 470s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Stream0/jobstore) 470s _______________________ TestDocker.testDockerLogs_Demux ________________________ 470s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 470s result: TResult | None = func() 470s ~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 470s lambda: runtest_hook(item=item, **kwds), 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 470s yield 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 470s return result.get_result() 470s ~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 470s raise exc.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 470s res = yield 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 470s item.runtest() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 470s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 470s result = testfunction(**testargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 369, in testDockerLogs_Demux 470s self.testDockerLogs(tmp_path, stream=False, demux=True) 470s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 470s rv = Job.Runner.startToil(A, options) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 470s return toil.start(job) 470s ~~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 470s return self._runMainLoop(rootJobDescription) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 470s ).run() 470s ~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 470s raise FailedJobsException( 470s ...<3 lines>... 470s ) 470s 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-0qs6m4d8 v6 470s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v6" follows: 470s =========> 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v4 470s [2026-01-30T23:43:22+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v4 470s [2026-01-30T23:43:22+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 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. 470s [2026-01-30T23:43:22+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:22+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s ----------------------------- Captured stderr call ----------------------------- 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of c032e959-35c6-4c44-b739-95f7a34be61f in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux0/jobstore 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.lib.history] Workflow c032e959-35c6-4c44-b739-95f7a34be61f is a run of 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:43:21+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-0qs6m4d8. 470s [2026-01-30T23:43:21+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v1 470s Exit reason: None 470s [2026-01-30T23:43:21+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v2 470s [2026-01-30T23:43:21+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-0qs6m4d8" follows: 470s =========> 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v1 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v1 470s [2026-01-30T23:43:21+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 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. 470s [2026-01-30T23:43:21+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:21+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:43:21+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v2 with ID kind-_testDockerLogsFn/instance-0qs6m4d8 to 1 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:43:21+0000] [Thread-45 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:43:21: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 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. 470s [2026-01-30T23:43:22+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-0qs6m4d8. 470s [2026-01-30T23:43:22+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v3 470s Exit reason: None 470s [2026-01-30T23:43:22+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v5 470s [2026-01-30T23:43:22+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-0qs6m4d8" follows: 470s =========> 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v4 470s [2026-01-30T23:43:22+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v4 470s [2026-01-30T23:43:22+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 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. 470s [2026-01-30T23:43:22+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:22+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:43:22+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v5 with ID kind-_testDockerLogsFn/instance-0qs6m4d8 to 0 470s [2026-01-30T23:43:22+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v6 is completely failed 470s [2026-01-30T23:43:22+0000] [Thread-45 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:43:22: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 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. 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v6 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.lib.history] Workflow c032e959-35c6-4c44-b739-95f7a34be61f stopped. Success: False 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux0/jobstore) 470s ------------------------------ Captured log call ------------------------------- 470s INFO  toil.lib.history:history.py:369 Recording workflow creation of c032e959-35c6-4c44-b739-95f7a34be61f in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux0/jobstore 470s INFO  toil.lib.history:history.py:399 Workflow c032e959-35c6-4c44-b739-95f7a34be61f is a run of 470s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s 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-0qs6m4d8. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v1 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v2 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-0qs6m4d8" follows: 470s =========> 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v1 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v1 470s [2026-01-30T23:43:21+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 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. 470s [2026-01-30T23:43:21+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:21+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v2 with ID kind-_testDockerLogsFn/instance-0qs6m4d8 to 1 470s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:43:21: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 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. 470s 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-0qs6m4d8. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v3 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v5 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-0qs6m4d8" follows: 470s =========> 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v4 470s [2026-01-30T23:43:22+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v4 470s [2026-01-30T23:43:22+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 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. 470s [2026-01-30T23:43:22+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:22+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v5 with ID kind-_testDockerLogsFn/instance-0qs6m4d8 to 0 470s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v6 is completely failed 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:43:22: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 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. 470s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 470s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v6 470s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 470s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 470s INFO  toil.lib.history:history.py:530 Workflow c032e959-35c6-4c44-b739-95f7a34be61f stopped. Success: False 470s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux0/jobstore) 470s ____________________ TestDocker.testDockerLogs_Demux_Stream ____________________ 470s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 470s result: TResult | None = func() 470s ~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 470s lambda: runtest_hook(item=item, **kwds), 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 470s yield 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 470s return result.get_result() 470s ~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 470s raise exc.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 470s res = yield 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 470s item.runtest() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 470s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 470s result = testfunction(**testargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 372, in testDockerLogs_Demux_Stream 470s self.testDockerLogs(tmp_path, stream=True, demux=True) 470s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 470s rv = Job.Runner.startToil(A, options) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 470s return toil.start(job) 470s ~~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 470s return self._runMainLoop(rootJobDescription) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 470s ).run() 470s ~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 470s raise FailedJobsException( 470s ...<3 lines>... 470s ) 470s 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-i80eael6 v6 470s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v6" follows: 470s =========> 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v4 470s [2026-01-30T23:43:26+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v4 470s [2026-01-30T23:43:26+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 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. 470s [2026-01-30T23:43:26+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:26+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s ----------------------------- Captured stderr call ----------------------------- 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 4de136e8-313d-4e21-ad7a-05b921106b9c in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux_Stream0/jobstore 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.lib.history] Workflow 4de136e8-313d-4e21-ad7a-05b921106b9c is a run of 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:43:25+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-i80eael6. 470s [2026-01-30T23:43:25+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v1 470s Exit reason: None 470s [2026-01-30T23:43:25+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v2 470s [2026-01-30T23:43:25+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-i80eael6" follows: 470s =========> 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v1 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v1 470s [2026-01-30T23:43:25+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 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. 470s [2026-01-30T23:43:25+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:25+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:43:25+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v2 with ID kind-_testDockerLogsFn/instance-i80eael6 to 1 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:43:25+0000] [Thread-49 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:43:25: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 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. 470s [2026-01-30T23:43:26+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-i80eael6. 470s [2026-01-30T23:43:26+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v3 470s Exit reason: None 470s [2026-01-30T23:43:26+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v5 470s [2026-01-30T23:43:26+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-i80eael6" follows: 470s =========> 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v4 470s [2026-01-30T23:43:26+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v4 470s [2026-01-30T23:43:26+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 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. 470s [2026-01-30T23:43:26+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:26+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:43:26+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v5 with ID kind-_testDockerLogsFn/instance-i80eael6 to 0 470s [2026-01-30T23:43:26+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v6 is completely failed 470s [2026-01-30T23:43:26+0000] [Thread-49 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:43:26: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 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. 470s [2026-01-30T23:43:29+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s [2026-01-30T23:43:29+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 470s [2026-01-30T23:43:29+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v6 470s [2026-01-30T23:43:29+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 470s [2026-01-30T23:43:29+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 470s [2026-01-30T23:43:29+0000] [MainThread] [I] [toil.lib.history] Workflow 4de136e8-313d-4e21-ad7a-05b921106b9c stopped. Success: False 470s [2026-01-30T23:43:29+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux_Stream0/jobstore) 470s ------------------------------ Captured log call ------------------------------- 470s INFO  toil.lib.history:history.py:369 Recording workflow creation of 4de136e8-313d-4e21-ad7a-05b921106b9c in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux_Stream0/jobstore 470s INFO  toil.lib.history:history.py:399 Workflow 4de136e8-313d-4e21-ad7a-05b921106b9c is a run of 470s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s 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-i80eael6. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v1 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v2 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-i80eael6" follows: 470s =========> 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v1 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v1 470s [2026-01-30T23:43:25+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 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. 470s [2026-01-30T23:43:25+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:25+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v2 with ID kind-_testDockerLogsFn/instance-i80eael6 to 1 470s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 470s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:43:25: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 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. 470s 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-i80eael6. 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v3 470s Exit reason: None 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v5 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-i80eael6" follows: 470s =========> 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v4 470s [2026-01-30T23:43:26+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v4 470s [2026-01-30T23:43:26+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 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. 470s [2026-01-30T23:43:26+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:26+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v5 with ID kind-_testDockerLogsFn/instance-i80eael6 to 0 470s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v6 is completely failed 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:43:26: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 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. 470s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 470s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v6 470s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 470s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 470s INFO  toil.lib.history:history.py:530 Workflow 4de136e8-313d-4e21-ad7a-05b921106b9c stopped. Success: False 470s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testDockerLogs_Demux_Stream0/jobstore) 470s __ TestSingleMachinePromisedRequirements.testPromisesWithJobStoreFileObjects ___ 470s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 470s result: TResult | None = func() 470s ~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 470s lambda: runtest_hook(item=item, **kwds), 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 470s yield 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 470s return result.get_result() 470s ~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 470s raise exc.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 470s res = yield 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 470s item.runtest() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 470s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 470s result = testfunction(**testargs) 470s File "/usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py", line 145, in testPromisesWithJobStoreFileObjects 470s Job.Runner.startToil(F1, self.getOptions(tmp_path, caching=caching)) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 470s return toil.start(job) 470s ~~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 470s return self._runMainLoop(rootJobDescription) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 470s ).run() 470s ~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 470s raise FailedJobsException( 470s ...<3 lines>... 470s ) 470s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore' contains 2 failed jobs: '_writer' kind-_writer/instance-m_dq_2rc v4, '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8 470s Log from job "'_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8" follows: 470s =========> 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '03001f5d-117e-4c91-9cbb-a0fb5b5551fd', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp2uq1k373', '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} 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb/deferred/funcqfazzvrg 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.worker] Parsed job description 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:18+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. 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:18+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. 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore'. 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6) from description '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6) with ID (kind-EncapsulatedJob/instance-sxnjxw3q). 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6) with ID (kind-EncapsulatedJob/instance-sxnjxw3q) which wants 2147483648 of our 98496815104 bytes. 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98496815104 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98496815104 bytes 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:18+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 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. 470s [2026-01-30T23:45:18+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 470s self.evaluatePromisedRequirements() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 470s ].getValue() 470s ~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 470s return func(*self._args) 470s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 470s 470s [2026-01-30T23:45:18+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [pydot] pydot initializing 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [pydot] pydot 4.0.1 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [pydot.core] pydot core module initializing 470s <========= 470s ----------------------------- Captured stderr call ----------------------------- 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.common] Initialized default configuration: {"config_version": 1.0} 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.batchSystems.options] Add options for aws_batch batch system 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.batchSystems.options] Add options for single_machine batch system 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.batchSystems.options] Add options for grid_engine batch system 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.batchSystems.options] Add options for lsf batch system 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.batchSystems.options] Add options for slurm batch system 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.batchSystems.options] Add options for torque batch system 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'test', 'cwltest', 'urllib3', 'docker', 'rdflib', 'humanfriendly', 'boto', 'asyncio', 'boto3', 'bcdocs', 'botocore', 'debugWorkflow', 'cachecontrol', 'concurrent', 'dill', 'requests', 'salad'} 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.statsAndLogging] Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'test', 'cwltest', 'urllib3', 'docker', 'rdflib', 'humanfriendly', 'boto', 'asyncio', 'boto3', 'bcdocs', 'botocore', 'debugWorkflow', 'cachecontrol', 'concurrent', 'dill', 'requests', 'salad'} 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.statsAndLogging] Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.common] Initialized default configuration: {"config_version": 1.0} 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.batchSystems.options] Add options for aws_batch batch system 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.batchSystems.options] Add options for single_machine batch system 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.batchSystems.options] Add options for grid_engine batch system 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.batchSystems.options] Add options for lsf batch system 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.batchSystems.options] Add options for slurm batch system 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.batchSystems.options] Add options for torque batch system 470s [2026-01-30T23:45:16+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-gw2/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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} 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore'. 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.jobStores.abstractJobStore] The workflow ID is: '03001f5d-117e-4c91-9cbb-a0fb5b5551fd' 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 03001f5d-117e-4c91-9cbb-a0fb5b5551fd in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.lib.history] Workflow 03001f5d-117e-4c91-9cbb-a0fb5b5551fd is a run of 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.common] Using the single machine batch system 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.common] Created the workflow directory for this machine at /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/workdir/toilwf-87ccc014276c54d4ab5856eebd22a1fb 470s [2026-01-30T23:45:16+0000] [Thread-76 (daddy)] [D] [toil.batchSystems.singleMachine] Started daddy thread for batch system 130508088108624. 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Started batch system 130508088108624 in normal mode. 470s [2026-01-30T23:45:16+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. 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.common] No user script to auto-deploy. 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.common] Written the environment for the jobs to the environment file 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.common] Caching all jobs in job store 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.common] 0 jobs downloaded. 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-dc34ab22b4504247935b85624ae5cb4f/stream for result of '_writer' TemporaryID(5bb50958-9cdd-4450-ad03-927d2aa0b43f) v0 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Saving graph of 5 jobs, 5 non-service, 5 new 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Processing job 'Job' kind-Job/instance-9oj8vefh v0 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Processing job '_follower' kind-_follower/instance-71jo1xfx v0 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-d0239cfeb8a24e3ba06452d0b6ae10d9/stream for result of '_writer' kind-_writer/instance-m_dq_2rc v0 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-2f7b415a02aa442c9d3707fc141300d0/stream for result of '_writer' kind-_writer/instance-9bhqmclq v0 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v0 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-9bhqmclq v0 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-m_dq_2rc v0 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] New job version: 'Job' kind-Job/instance-9oj8vefh v1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-_follower/instance-71jo1xfx v1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-9bhqmclq v1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-m_dq_2rc v1 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '03001f5d-117e-4c91-9cbb-a0fb5b5551fd', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp2uq1k373', '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} 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.bus] Listening for message topic: toil.bus.JobUpdatedMessage 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.toilState] Found job to run: kind-_writer/instance-m_dq_2rc, with body: True, with checkpoint: False, with services: False, with no next successors: False 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-m_dq_2rc', result_status=0) 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.leader] Found 1 jobs to start and 0 jobs with successors to run 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.leader] Checked batch system has no running jobs and no updated jobs 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.serviceManager] Initializing service manager 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-m_dq_2rc v1 with result status: 0 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore kind-_writer/instance-m_dq_2rc with disk: 2.0 Gi, memory: 2.0 Gi, cores: 2.0, accelerators: [], preemptible: False 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.leader] Issued job '_writer' kind-_writer/instance-m_dq_2rc v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 2, accelerators: [], preemptible: False 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_writer', job_id='kind-_writer/instance-m_dq_2rc', toil_batch_id=1) 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 470s [2026-01-30T23:45:16+0000] [Thread-76 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore kind-_writer/instance-m_dq_2rc 470s [2026-01-30T23:45:16+0000] [Thread-76 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 1 as child 11077 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'urllib3', 'boto3', 'asyncio', 'docker', 'botocore', 'requests', 'concurrent', 'boto', 'dill'} 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.worker] Worker started for job _writer... 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.common] Obtained node ID d186161f45b648b99615a7187522b0d8 from file /var/lib/dbus/machine-id 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/workdir/toilwf-87ccc014276c54d4ab5856eebd22a1fb/d69e/worker_log.txt 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb/deferred/funcuk5dfc1p 470s [2026-01-30T23:45:16+0000] [Thread-79 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:45:16: Job '_writer' kind-_writer/instance-m_dq_2rc v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:16+0000] [Thread-79 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:45:16: Job '_writer' kind-_writer/instance-m_dq_2rc v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:16+0000] [Thread-79 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Received Toil worker log. Disable debug level logging to hide this output 470s [2026-01-30T23:45:16+0000] [Thread-79 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Log from job "JobFunctionWrappingJob" follows: 470s =========> 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '03001f5d-117e-4c91-9cbb-a0fb5b5551fd', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp2uq1k373', '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} 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb/deferred/funcuk5dfc1p 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.worker] Parsed job description 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-m_dq_2rc v1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:16+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. 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:16+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. 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-m_dq_2rc v1) from description '_writer' kind-_writer/instance-m_dq_2rc v1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-m_dq_2rc v1) with ID (kind-_writer/instance-m_dq_2rc). 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_writer' kind-_writer/instance-m_dq_2rc v1) with ID (kind-_writer/instance-m_dq_2rc) which wants 2147483648 of our 98496815104 bytes. 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98496815104 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 0 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98496815104 bytes 470s [2026-01-30T23:45:16+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). 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Hardlinked file /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/workdir/toilwf-87ccc014276c54d4ab5856eebd22a1fb/d69e/job/tmp5vb3oc0u.tmp into cache at /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/workdir/toilwf-87ccc014276c54d4ab5856eebd22a1fb/cache-03001f5d-117e-4c91-9cbb-a0fb5b5551fd/tmphptp0n8kea3a343e9b6eebf0be58e96512999278fcb7ad9a; deferring write to job store 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-dc34ab22b4504247935b85624ae5cb4f/stream from Job('_writer' kind-_writer/instance-m_dq_2rc v1) with a 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-d0239cfeb8a24e3ba06452d0b6ae10d9/stream from Job('_writer' kind-_writer/instance-m_dq_2rc v1) with a 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-m_dq_2rc v1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-m_dq_2rc v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-m_dq_2rc v1 forked from '_writer' kind-_writer/instance-m_dq_2rc v1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-m_dq_2rc v2 470s [2026-01-30T23:45:16+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-m_dq_2rc v2 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-m_dq_2rc v2 would chain to ID kind-_writer/instance-9bhqmclq 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Chaining from '_writer' kind-_writer/instance-m_dq_2rc v2 to '_writer' kind-_writer/instance-9bhqmclq v1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] '_writer' kind-_writer/instance-9bhqmclq v1 is adopting successor phases from '_writer' kind-_writer/instance-m_dq_2rc v2 of: [] 470s [2026-01-30T23:45:16+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Actually executing upload for file files/for-job/kind-_writer/instance-m_dq_2rc/file-c356ca49729446079e00522da8ff10c0/tmp5vb3oc0u.tmp 470s [2026-01-30T23:45:16+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-m_dq_2rc v1 470s [2026-01-30T23:45:16+0000] [Thread-2 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-m_dq_2rc v2 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-m_dq_2rc v2) with ID (kind-_writer/instance-m_dq_2rc). 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-m_dq_2rc v2 forked from '_writer' kind-_writer/instance-m_dq_2rc v2 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-m_dq_2rc v3 470s [2026-01-30T23:45:16+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.worker] Starting the next job 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-m_dq_2rc v3 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:16+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-m_dq_2rc v2 470s [2026-01-30T23:45:16+0000] [Thread-3 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-m_dq_2rc v3 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-m_dq_2rc v3) from description '_writer' kind-_writer/instance-m_dq_2rc v3 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-m_dq_2rc v3) with ID (kind-_writer/instance-m_dq_2rc). 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_writer' kind-_writer/instance-m_dq_2rc v3) with ID (kind-_writer/instance-m_dq_2rc) which wants 2147483648 of our 98496815104 bytes. 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98496815104 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1024 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98496815104 bytes 470s [2026-01-30T23:45:16+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). 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Hardlinked file /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/workdir/toilwf-87ccc014276c54d4ab5856eebd22a1fb/d69e/job/tmpc28vgrd7.tmp into cache at /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/workdir/toilwf-87ccc014276c54d4ab5856eebd22a1fb/cache-03001f5d-117e-4c91-9cbb-a0fb5b5551fd/tmprtuakbgb9cc2c68124b81bcdc71525483eeb38c6ccfd385f; deferring write to job store 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-2f7b415a02aa442c9d3707fc141300d0/stream from Job('_writer' kind-_writer/instance-m_dq_2rc v3) with a 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-m_dq_2rc v3 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-m_dq_2rc v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-m_dq_2rc v3 forked from '_writer' kind-_writer/instance-m_dq_2rc v3 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-m_dq_2rc v4 470s [2026-01-30T23:45:16+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-m_dq_2rc v4 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-m_dq_2rc v4 would chain to ID kind-EncapsulatedJob/instance-sxnjxw3q 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.worker] Preemptibility is different for the next job, returning to the leader 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Not chaining from job '_writer' kind-_writer/instance-m_dq_2rc v4 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/workdir/toilwf-87ccc014276c54d4ab5856eebd22a1fb/d69e. Set --cleanWorkDir to retain this log 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 0.191399 seconds 470s [2026-01-30T23:45:16+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Actually executing upload for file files/for-job/kind-_writer/instance-m_dq_2rc/file-6c624ca708e54e6f956267523698c56c/tmpc28vgrd7.tmp 470s [2026-01-30T23:45:16+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-m_dq_2rc v3 470s [2026-01-30T23:45:16+0000] [Thread-4 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-m_dq_2rc v4 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [pydot] pydot initializing 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [pydot] pydot 4.0.1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [pydot.core] pydot core module initializing 470s <========= 470s [2026-01-30T23:45:16+0000] [Thread-76 (daddy)] [D] [toil.batchSystems.singleMachine] Child 11077 for job 1 succeeded 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 1 with exit value: 0 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.leader] Job ended: '_writer' kind-_writer/instance-m_dq_2rc v1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_writer', job_id='kind-_writer/instance-m_dq_2rc', exit_code=0) 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=1, external_batch_id='11077', batch_system='SingleMachineBatchSystem') 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.leader] Job '_writer' kind-_writer/instance-m_dq_2rc v1 continues to exist (i.e. has more to do) 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-m_dq_2rc', result_status=0) 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.leader] Added job: '_writer' kind-_writer/instance-m_dq_2rc v4 to updated jobs 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-m_dq_2rc v4 with result status: 0 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.leader] Job: kind-_writer/instance-m_dq_2rc has 1 successors to schedule 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.toilState] Successors: 1 more for kind-_writer/instance-m_dq_2rc, now have 1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.leader] Added job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 as coming after job '_writer' kind-_writer/instance-m_dq_2rc v4 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-sxnjxw3q with disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.leader] Issued job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 with job batch system ID: 2 and disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-sxnjxw3q', toil_batch_id=2) 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 470s [2026-01-30T23:45:16+0000] [Thread-76 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-sxnjxw3q 470s [2026-01-30T23:45:16+0000] [Thread-76 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 2 as child 11173 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'botocore', 'asyncio', 'boto', 'dill', 'requests', 'docker', 'boto3', 'concurrent', 'urllib3'} 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.worker] Worker started for job EncapsulatedJob... 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.common] Obtained node ID d186161f45b648b99615a7187522b0d8 from file /var/lib/dbus/machine-id 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/workdir/toilwf-87ccc014276c54d4ab5856eebd22a1fb/948e/worker_log.txt 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v4 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb/deferred/funcb79xw9a4 470s [2026-01-30T23:45:17+0000] [Thread-76 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-sxnjxw3q. 470s [2026-01-30T23:45:17+0000] [Thread-76 (daddy)] [D] [toil.batchSystems.singleMachine] Child 11173 for job 2 succeeded 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 2 with exit value: 1 470s [2026-01-30T23:45:17+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 470s Exit reason: None 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-sxnjxw3q', exit_code=1) 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=2, external_batch_id='11173', batch_system='SingleMachineBatchSystem') 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.leader] Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 continues to exist (i.e. has more to do) 470s [2026-01-30T23:45:17+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v4 470s [2026-01-30T23:45:17+0000] [MainThread] [W] [toil.leader] Log from job "kind-EncapsulatedJob/instance-sxnjxw3q" follows: 470s =========> 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '03001f5d-117e-4c91-9cbb-a0fb5b5551fd', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp2uq1k373', '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} 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb/deferred/funcb79xw9a4 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.worker] Parsed job description 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] Working on job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:17+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. 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:17+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. 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] Loaded body Job('EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1) from description 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1) with ID (kind-EncapsulatedJob/instance-sxnjxw3q). 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1) with ID (kind-EncapsulatedJob/instance-sxnjxw3q) which wants 1000000 of our 98496815104 bytes. 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98496815104 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 1000000 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98496815104 bytes 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 forked from 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] Skip ahead to job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v2 470s [2026-01-30T23:45:17+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 470s [2026-01-30T23:45:17+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 470s [2026-01-30T23:45:17+0000] [Thread-2 (startCommitThread)] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v2 470s [2026-01-30T23:45:17+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v2 used 6.59x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] Completed body for 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v2 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.worker] 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v2 would chain to ID kind-_follower/instance-71jo1xfx 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] Chaining from 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v2 to '_follower' kind-_follower/instance-71jo1xfx v1 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] '_follower' kind-_follower/instance-71jo1xfx v1 is adopting successor phases from 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v2 of: [{'kind-Job/instance-9oj8vefh'}] 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v2) with ID (kind-EncapsulatedJob/instance-sxnjxw3q). 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v2 forked from '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v2 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3 470s [2026-01-30T23:45:17+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 470s [2026-01-30T23:45:17+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v2 470s [2026-01-30T23:45:17+0000] [Thread-3 (startCommitThread)] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.worker] Starting the next job 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore'. 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3) from description '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3) with ID (kind-EncapsulatedJob/instance-sxnjxw3q). 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3) with ID (kind-EncapsulatedJob/instance-sxnjxw3q) which wants 1000000 of our 98496815104 bytes. 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98496815104 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 1000000 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98496815104 bytes 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:17+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3 used 5.57x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s [2026-01-30T23:45:17+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 470s self.evaluatePromisedRequirements() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 470s ].getValue() 470s ~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 470s return func(*self._args) 470s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 470s 470s [2026-01-30T23:45:17+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [pydot] pydot initializing 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [pydot] pydot 4.0.1 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [pydot.core] pydot core module initializing 470s <========= 470s [2026-01-30T23:45:17+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v4 with ID kind-EncapsulatedJob/instance-sxnjxw3q to 1 470s [2026-01-30T23:45:17+0000] [MainThread] [W] [toil.job] We have increased the default memory of the failed job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v4 to 2147483648 bytes 470s [2026-01-30T23:45:17+0000] [MainThread] [W] [toil.job] We have increased the disk of the failed job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v4 to the default of 2147483648 bytes 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v5 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-sxnjxw3q', result_status=1) 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.leader] Added job: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v5 to updated jobs 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.leader] Updating status of job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v5 with result status: 1 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-sxnjxw3q with disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.leader] Issued job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v5 with job batch system ID: 3 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-sxnjxw3q', toil_batch_id=3) 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 470s [2026-01-30T23:45:17+0000] [Thread-76 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-sxnjxw3q 470s [2026-01-30T23:45:17+0000] [Thread-76 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 3 as child 11199 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'urllib3', 'asyncio', 'botocore', 'docker', 'requests', 'boto', 'dill', 'boto3', 'concurrent'} 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.worker] Worker started for job _follower... 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.common] Obtained node ID d186161f45b648b99615a7187522b0d8 from file /var/lib/dbus/machine-id 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/workdir/toilwf-87ccc014276c54d4ab5856eebd22a1fb/b6fb/worker_log.txt 470s [2026-01-30T23:45:17+0000] [Thread-79 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:45:17: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 470s [2026-01-30T23:45:17+0000] [Thread-79 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:45:17: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v2 used 6.59x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s [2026-01-30T23:45:17+0000] [Thread-79 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:45:17: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 470s [2026-01-30T23:45:17+0000] [Thread-79 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:45:17: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3 used 5.57x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v7 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb/deferred/funcqfazzvrg 470s [2026-01-30T23:45:18+0000] [Thread-76 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-sxnjxw3q. 470s [2026-01-30T23:45:18+0000] [Thread-76 (daddy)] [D] [toil.batchSystems.singleMachine] Child 11199 for job 3 succeeded 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 3 with exit value: 1 470s [2026-01-30T23:45:18+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v5 470s Exit reason: None 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-sxnjxw3q', exit_code=1) 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=3, external_batch_id='11199', batch_system='SingleMachineBatchSystem') 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.leader] Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v5 continues to exist (i.e. has more to do) 470s [2026-01-30T23:45:18+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v7 470s [2026-01-30T23:45:18+0000] [MainThread] [W] [toil.leader] Log from job "kind-EncapsulatedJob/instance-sxnjxw3q" follows: 470s =========> 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '03001f5d-117e-4c91-9cbb-a0fb5b5551fd', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp2uq1k373', '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} 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb/deferred/funcqfazzvrg 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.worker] Parsed job description 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:18+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. 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:18+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. 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore'. 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6) from description '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6) with ID (kind-EncapsulatedJob/instance-sxnjxw3q). 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6) with ID (kind-EncapsulatedJob/instance-sxnjxw3q) which wants 2147483648 of our 98496815104 bytes. 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98496815104 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98496815104 bytes 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:18+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 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. 470s [2026-01-30T23:45:18+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 470s self.evaluatePromisedRequirements() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 470s ].getValue() 470s ~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 470s return func(*self._args) 470s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 470s 470s [2026-01-30T23:45:18+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [pydot] pydot initializing 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [pydot] pydot 4.0.1 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [pydot.core] pydot core module initializing 470s <========= 470s [2026-01-30T23:45:18+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v7 with ID kind-EncapsulatedJob/instance-sxnjxw3q to 0 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-sxnjxw3q', result_status=1) 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.leader] Added job: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8 to updated jobs 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.leader] Updating status of job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8 with result status: 1 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-sxnjxw3q') 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.leader] Found new failed successors: kind-Job/instance-9oj8vefh of job: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.leader] Totally failed job: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8 is marking direct predecessor: '_writer' kind-_writer/instance-m_dq_2rc v4 as having failed jobs 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.leader] Cleaning the predecessors of kind-EncapsulatedJob/instance-sxnjxw3q 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.toilState] Successors: one fewer for kind-_writer/instance-m_dq_2rc, now have 0 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-m_dq_2rc', result_status=0) 470s [2026-01-30T23:45:18+0000] [MainThread] [W] [toil.leader] Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8 is completely failed 470s [2026-01-30T23:45:18+0000] [Thread-79 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:45:18: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:18+0000] [Thread-79 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:45:18: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 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. 470s [2026-01-30T23:45:20+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s [2026-01-30T23:45:20+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-m_dq_2rc v4 with result status: 0 470s [2026-01-30T23:45:20+0000] [MainThread] [D] [toil.leader] Job kind-_writer/instance-m_dq_2rc is being processed as completely failed 470s [2026-01-30T23:45:20+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_writer', job_id='kind-_writer/instance-m_dq_2rc') 470s [2026-01-30T23:45:20+0000] [MainThread] [D] [toil.leader] Found new failed successors: of job: '_writer' kind-_writer/instance-m_dq_2rc v4 470s [2026-01-30T23:45:22+0000] [MainThread] [D] [toil.leader] Finished the main loop: no jobs left to run. 470s [2026-01-30T23:45:22+0000] [MainThread] [D] [toil.serviceManager] Waiting for service manager thread to finish ... 470s [2026-01-30T23:45:22+0000] [Thread-78 (__start_services)] [D] [toil.serviceManager] Received signal to quit starting services. 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.serviceManager] ... finished shutting down the service manager. Took 1.2036736011505127 seconds 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.statsAndLogging] Waiting for stats and logging collator thread to finish ... 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.statsAndLogging] ... finished collating stats and logs. Took 0.0004417896270751953 seconds 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.leader] Finished toil run with 2 failed jobs. 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_writer' kind-_writer/instance-m_dq_2rc v4 '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.common] Shutting down batch system ... 470s [2026-01-30T23:45:23+0000] [Thread-76 (daddy)] [D] [toil.batchSystems.singleMachine] Daddy thread cleaning up 0 remaining children for batch system 130508088108624... 470s [2026-01-30T23:45:23+0000] [Thread-76 (daddy)] [D] [toil.batchSystems.singleMachine] Daddy thread for batch system 130508088108624 finishing because no children should now exist 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Attempting worker cleanup 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Cleaning up deferred functions system 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb/deferred/funczjvi3nd3 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb/deferred/funczjvi3nd3 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Connecting to latest caching database cache-0.db for cleanup 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Deleting workflow directory /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/workdir/toilwf-87ccc014276c54d4ab5856eebd22a1fb 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Deleting coordination directory /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.common] ... finished shutting down the batch system in 0.01835036277770996 seconds. 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.lib.history] Workflow 03001f5d-117e-4c91-9cbb-a0fb5b5551fd stopped. Success: False 470s ------------------------------ Captured log call ------------------------------- 470s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s DEBUG  toil.common:common.py:796 Initialized default configuration: {"config_version": 1.0} 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for aws_batch batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for single_machine batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for grid_engine batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for lsf batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for slurm batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for torque batch system 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:488 Suppressing the following loggers: {'test', 'cwltest', 'urllib3', 'docker', 'rdflib', 'humanfriendly', 'boto', 'asyncio', 'boto3', 'bcdocs', 'botocore', 'debugWorkflow', 'cachecontrol', 'concurrent', 'dill', 'requests', 'salad'} 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:447 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:488 Suppressing the following loggers: {'test', 'cwltest', 'urllib3', 'docker', 'rdflib', 'humanfriendly', 'boto', 'asyncio', 'boto3', 'bcdocs', 'botocore', 'debugWorkflow', 'cachecontrol', 'concurrent', 'dill', 'requests', 'salad'} 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:447 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 470s DEBUG  toil.common:common.py:796 Initialized default configuration: {"config_version": 1.0} 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for aws_batch batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for single_machine batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for grid_engine batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for lsf batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for slurm batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for torque batch system 470s 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-gw2/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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} 470s DEBUG  toil.jobStores.fileJobStore:fileJobStore.py:93 Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore'. 470s DEBUG  toil.jobStores.abstractJobStore:abstractJobStore.py:212 The workflow ID is: '03001f5d-117e-4c91-9cbb-a0fb5b5551fd' 470s INFO  toil.lib.history:history.py:369 Recording workflow creation of 03001f5d-117e-4c91-9cbb-a0fb5b5551fd in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore 470s INFO  toil.lib.history:history.py:399 Workflow 03001f5d-117e-4c91-9cbb-a0fb5b5551fd is a run of 470s DEBUG  toil.common:common.py:1346 Using the single machine batch system 470s DEBUG  toil.common:common.py:1723 Created the workflow directory for this machine at /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/workdir/toilwf-87ccc014276c54d4ab5856eebd22a1fb 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:247 Started daddy thread for batch system 130508088108624. 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:229 Started batch system 130508088108624 in normal mode. 470s 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. 470s DEBUG  toil.common:common.py:1409 No user script to auto-deploy. 470s DEBUG  toil.common:common.py:1576 Written the environment for the jobs to the environment file 470s DEBUG  toil.common:common.py:1580 Caching all jobs in job store 470s DEBUG  toil.common:common.py:1584 0 jobs downloaded. 470s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-dc34ab22b4504247935b85624ae5cb4f/stream for result of '_writer' TemporaryID(5bb50958-9cdd-4450-ad03-927d2aa0b43f) v0 470s DEBUG  toil.job:job.py:3000 Saving graph of 5 jobs, 5 non-service, 5 new 470s DEBUG  toil.job:job.py:3023 Processing job 'Job' kind-Job/instance-9oj8vefh v0 470s DEBUG  toil.job:job.py:3023 Processing job '_follower' kind-_follower/instance-71jo1xfx v0 470s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-d0239cfeb8a24e3ba06452d0b6ae10d9/stream for result of '_writer' kind-_writer/instance-m_dq_2rc v0 470s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-2f7b415a02aa442c9d3707fc141300d0/stream for result of '_writer' kind-_writer/instance-9bhqmclq v0 470s DEBUG  toil.job:job.py:3023 Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v0 470s DEBUG  toil.job:job.py:3023 Processing job '_writer' kind-_writer/instance-9bhqmclq v0 470s DEBUG  toil.job:job.py:3023 Processing job '_writer' kind-_writer/instance-m_dq_2rc v0 470s DEBUG  toil.job:job.py:1507 New job version: 'Job' kind-Job/instance-9oj8vefh v1 470s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-_follower/instance-71jo1xfx v1 470s DEBUG  toil.job:job.py:1507 New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 470s DEBUG  toil.job:job.py:1507 New job version: '_writer' kind-_writer/instance-9bhqmclq v1 470s DEBUG  toil.job:job.py:1507 New job version: '_writer' kind-_writer/instance-m_dq_2rc v1 470s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s DEBUG  toil:__init__.py:481 Configuration: {'cwl': False, 'workflowID': '03001f5d-117e-4c91-9cbb-a0fb5b5551fd', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp2uq1k373', '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} 470s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 470s DEBUG  toil.bus:bus.py:403 Listening for message topic: toil.bus.JobUpdatedMessage 470s DEBUG  toil.toilState:toilState.py:322 Found job to run: kind-_writer/instance-m_dq_2rc, with body: True, with checkpoint: False, with services: False, with no next successors: False 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-m_dq_2rc', result_status=0) 470s DEBUG  toil.leader:leader.py:145 Found 1 jobs to start and 0 jobs with successors to run 470s DEBUG  toil.leader:leader.py:157 Checked batch system has no running jobs and no updated jobs 470s DEBUG  toil.serviceManager:serviceManager.py:35 Initializing service manager 470s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-m_dq_2rc v1 with result status: 0 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore kind-_writer/instance-m_dq_2rc with disk: 2.0 Gi, memory: 2.0 Gi, cores: 2.0, accelerators: [], preemptible: False 470s INFO  toil.leader:leader.py:1132 Issued job '_writer' kind-_writer/instance-m_dq_2rc v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 2, accelerators: [], preemptible: False 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_writer', job_id='kind-_writer/instance-m_dq_2rc', toil_batch_id=1) 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore kind-_writer/instance-m_dq_2rc 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 1 as child 11077 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:45:16: Job '_writer' kind-_writer/instance-m_dq_2rc v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:45:16: Job '_writer' kind-_writer/instance-m_dq_2rc v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:98 Received Toil worker log. Disable debug level logging to hide this output 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:101 Log from job "JobFunctionWrappingJob" follows: 470s =========> 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '03001f5d-117e-4c91-9cbb-a0fb5b5551fd', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp2uq1k373', '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} 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb/deferred/funcuk5dfc1p 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.worker] Parsed job description 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-m_dq_2rc v1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:16+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. 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:16+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. 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-m_dq_2rc v1) from description '_writer' kind-_writer/instance-m_dq_2rc v1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-m_dq_2rc v1) with ID (kind-_writer/instance-m_dq_2rc). 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_writer' kind-_writer/instance-m_dq_2rc v1) with ID (kind-_writer/instance-m_dq_2rc) which wants 2147483648 of our 98496815104 bytes. 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98496815104 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 0 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98496815104 bytes 470s [2026-01-30T23:45:16+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). 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Hardlinked file /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/workdir/toilwf-87ccc014276c54d4ab5856eebd22a1fb/d69e/job/tmp5vb3oc0u.tmp into cache at /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/workdir/toilwf-87ccc014276c54d4ab5856eebd22a1fb/cache-03001f5d-117e-4c91-9cbb-a0fb5b5551fd/tmphptp0n8kea3a343e9b6eebf0be58e96512999278fcb7ad9a; deferring write to job store 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-dc34ab22b4504247935b85624ae5cb4f/stream from Job('_writer' kind-_writer/instance-m_dq_2rc v1) with a 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-d0239cfeb8a24e3ba06452d0b6ae10d9/stream from Job('_writer' kind-_writer/instance-m_dq_2rc v1) with a 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-m_dq_2rc v1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-m_dq_2rc v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-m_dq_2rc v1 forked from '_writer' kind-_writer/instance-m_dq_2rc v1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-m_dq_2rc v2 470s [2026-01-30T23:45:16+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-m_dq_2rc v2 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-m_dq_2rc v2 would chain to ID kind-_writer/instance-9bhqmclq 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Chaining from '_writer' kind-_writer/instance-m_dq_2rc v2 to '_writer' kind-_writer/instance-9bhqmclq v1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] '_writer' kind-_writer/instance-9bhqmclq v1 is adopting successor phases from '_writer' kind-_writer/instance-m_dq_2rc v2 of: [] 470s [2026-01-30T23:45:16+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Actually executing upload for file files/for-job/kind-_writer/instance-m_dq_2rc/file-c356ca49729446079e00522da8ff10c0/tmp5vb3oc0u.tmp 470s [2026-01-30T23:45:16+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-m_dq_2rc v1 470s [2026-01-30T23:45:16+0000] [Thread-2 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-m_dq_2rc v2 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-m_dq_2rc v2) with ID (kind-_writer/instance-m_dq_2rc). 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-m_dq_2rc v2 forked from '_writer' kind-_writer/instance-m_dq_2rc v2 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-m_dq_2rc v3 470s [2026-01-30T23:45:16+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.worker] Starting the next job 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-m_dq_2rc v3 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:16+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-m_dq_2rc v2 470s [2026-01-30T23:45:16+0000] [Thread-3 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-m_dq_2rc v3 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-m_dq_2rc v3) from description '_writer' kind-_writer/instance-m_dq_2rc v3 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-m_dq_2rc v3) with ID (kind-_writer/instance-m_dq_2rc). 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_writer' kind-_writer/instance-m_dq_2rc v3) with ID (kind-_writer/instance-m_dq_2rc) which wants 2147483648 of our 98496815104 bytes. 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98496815104 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1024 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98496815104 bytes 470s [2026-01-30T23:45:16+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). 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Hardlinked file /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/workdir/toilwf-87ccc014276c54d4ab5856eebd22a1fb/d69e/job/tmpc28vgrd7.tmp into cache at /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/workdir/toilwf-87ccc014276c54d4ab5856eebd22a1fb/cache-03001f5d-117e-4c91-9cbb-a0fb5b5551fd/tmprtuakbgb9cc2c68124b81bcdc71525483eeb38c6ccfd385f; deferring write to job store 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-2f7b415a02aa442c9d3707fc141300d0/stream from Job('_writer' kind-_writer/instance-m_dq_2rc v3) with a 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-m_dq_2rc v3 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-m_dq_2rc v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-m_dq_2rc v3 forked from '_writer' kind-_writer/instance-m_dq_2rc v3 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-m_dq_2rc v4 470s [2026-01-30T23:45:16+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-m_dq_2rc v4 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-m_dq_2rc v4 would chain to ID kind-EncapsulatedJob/instance-sxnjxw3q 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [toil.worker] Preemptibility is different for the next job, returning to the leader 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Not chaining from job '_writer' kind-_writer/instance-m_dq_2rc v4 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/workdir/toilwf-87ccc014276c54d4ab5856eebd22a1fb/d69e. Set --cleanWorkDir to retain this log 470s [2026-01-30T23:45:16+0000] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 0.191399 seconds 470s [2026-01-30T23:45:16+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Actually executing upload for file files/for-job/kind-_writer/instance-m_dq_2rc/file-6c624ca708e54e6f956267523698c56c/tmpc28vgrd7.tmp 470s [2026-01-30T23:45:16+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-m_dq_2rc v3 470s [2026-01-30T23:45:16+0000] [Thread-4 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-m_dq_2rc v4 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [pydot] pydot initializing 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [pydot] pydot 4.0.1 470s [2026-01-30T23:45:16+0000] [MainThread] [D] [pydot.core] pydot core module initializing 470s <========= 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 11077 for job 1 succeeded 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 1 with exit value: 0 470s DEBUG  toil.leader:leader.py:846 Job ended: '_writer' kind-_writer/instance-m_dq_2rc v1 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_writer', job_id='kind-_writer/instance-m_dq_2rc', exit_code=0) 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=1, external_batch_id='11077', batch_system='SingleMachineBatchSystem') 470s DEBUG  toil.leader:leader.py:1455 Job '_writer' kind-_writer/instance-m_dq_2rc v1 continues to exist (i.e. has more to do) 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-m_dq_2rc', result_status=0) 470s DEBUG  toil.leader:leader.py:1620 Added job: '_writer' kind-_writer/instance-m_dq_2rc v4 to updated jobs 470s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 470s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-m_dq_2rc v4 with result status: 0 470s DEBUG  toil.leader:leader.py:506 Job: kind-_writer/instance-m_dq_2rc has 1 successors to schedule 470s DEBUG  toil.toilState:toilState.py:264 Successors: 1 more for kind-_writer/instance-m_dq_2rc, now have 1 470s DEBUG  toil.leader:leader.py:476 Added job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 as coming after job '_writer' kind-_writer/instance-m_dq_2rc v4 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-sxnjxw3q with disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 470s INFO  toil.leader:leader.py:1132 Issued job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 with job batch system ID: 2 and disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-sxnjxw3q', toil_batch_id=2) 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-sxnjxw3q 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 2 as child 11173 470s 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-gw2/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-sxnjxw3q. 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 11173 for job 2 succeeded 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 2 with exit value: 1 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 470s Exit reason: None 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-sxnjxw3q', exit_code=1) 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=2, external_batch_id='11173', batch_system='SingleMachineBatchSystem') 470s DEBUG  toil.leader:leader.py:1455 Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 continues to exist (i.e. has more to do) 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v4 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-EncapsulatedJob/instance-sxnjxw3q" follows: 470s =========> 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '03001f5d-117e-4c91-9cbb-a0fb5b5551fd', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp2uq1k373', '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} 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb/deferred/funcb79xw9a4 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.worker] Parsed job description 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] Working on job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:17+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. 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:17+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. 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] Loaded body Job('EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1) from description 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1) with ID (kind-EncapsulatedJob/instance-sxnjxw3q). 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1) with ID (kind-EncapsulatedJob/instance-sxnjxw3q) which wants 1000000 of our 98496815104 bytes. 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98496815104 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 1000000 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98496815104 bytes 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 forked from 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] Skip ahead to job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v2 470s [2026-01-30T23:45:17+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 470s [2026-01-30T23:45:17+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 470s [2026-01-30T23:45:17+0000] [Thread-2 (startCommitThread)] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v2 470s [2026-01-30T23:45:17+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v2 used 6.59x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] Completed body for 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v2 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.worker] 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v2 would chain to ID kind-_follower/instance-71jo1xfx 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] Chaining from 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v2 to '_follower' kind-_follower/instance-71jo1xfx v1 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] '_follower' kind-_follower/instance-71jo1xfx v1 is adopting successor phases from 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v2 of: [{'kind-Job/instance-9oj8vefh'}] 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v2) with ID (kind-EncapsulatedJob/instance-sxnjxw3q). 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v2 forked from '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v2 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3 470s [2026-01-30T23:45:17+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 470s [2026-01-30T23:45:17+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v2 470s [2026-01-30T23:45:17+0000] [Thread-3 (startCommitThread)] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.worker] Starting the next job 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore'. 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3) from description '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3) with ID (kind-EncapsulatedJob/instance-sxnjxw3q). 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3) with ID (kind-EncapsulatedJob/instance-sxnjxw3q) which wants 1000000 of our 98496815104 bytes. 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98496815104 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 1000000 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98496815104 bytes 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:17+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3 used 5.57x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s [2026-01-30T23:45:17+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 470s self.evaluatePromisedRequirements() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 470s ].getValue() 470s ~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 470s return func(*self._args) 470s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 470s 470s [2026-01-30T23:45:17+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [pydot] pydot initializing 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [pydot] pydot 4.0.1 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [pydot.core] pydot core module initializing 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v4 with ID kind-EncapsulatedJob/instance-sxnjxw3q to 1 470s WARNING  toil.job:job.py:1413 We have increased the default memory of the failed job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v4 to 2147483648 bytes 470s WARNING  toil.job:job.py:1421 We have increased the disk of the failed job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v4 to the default of 2147483648 bytes 470s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v5 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-sxnjxw3q', result_status=1) 470s DEBUG  toil.leader:leader.py:1620 Added job: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v5 to updated jobs 470s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s DEBUG  toil.leader:leader.py:606 Updating status of job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v5 with result status: 1 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-sxnjxw3q with disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 470s INFO  toil.leader:leader.py:1132 Issued job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v5 with job batch system ID: 3 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-sxnjxw3q', toil_batch_id=3) 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-sxnjxw3q 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 3 as child 11199 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:45:17: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:45:17: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-sxnjxw3q v2 used 6.59x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:45:17: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:45:17: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v3 used 5.57x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s 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-gw2/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-sxnjxw3q. 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 11199 for job 3 succeeded 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 3 with exit value: 1 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v5 470s Exit reason: None 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-sxnjxw3q', exit_code=1) 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=3, external_batch_id='11199', batch_system='SingleMachineBatchSystem') 470s DEBUG  toil.leader:leader.py:1455 Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v5 continues to exist (i.e. has more to do) 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v7 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-EncapsulatedJob/instance-sxnjxw3q" follows: 470s =========> 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '03001f5d-117e-4c91-9cbb-a0fb5b5551fd', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp2uq1k373', '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} 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb/deferred/funcqfazzvrg 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.worker] Parsed job description 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:18+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. 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:18+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. 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore'. 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6) from description '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6) with ID (kind-EncapsulatedJob/instance-sxnjxw3q). 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6) with ID (kind-EncapsulatedJob/instance-sxnjxw3q) which wants 2147483648 of our 98496815104 bytes. 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98496815104 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98496815104 bytes 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:18+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 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. 470s [2026-01-30T23:45:18+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 470s self.evaluatePromisedRequirements() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 470s ].getValue() 470s ~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 470s return func(*self._args) 470s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 470s 470s [2026-01-30T23:45:18+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [pydot] pydot initializing 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [pydot] pydot 4.0.1 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [pydot.core] pydot core module initializing 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v7 with ID kind-EncapsulatedJob/instance-sxnjxw3q to 0 470s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-sxnjxw3q', result_status=1) 470s DEBUG  toil.leader:leader.py:1620 Added job: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8 to updated jobs 470s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s DEBUG  toil.leader:leader.py:606 Updating status of job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8 with result status: 1 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-sxnjxw3q') 470s DEBUG  toil.leader:leader.py:1735 Found new failed successors: kind-Job/instance-9oj8vefh of job: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8 470s DEBUG  toil.leader:leader.py:1779 Totally failed job: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8 is marking direct predecessor: '_writer' kind-_writer/instance-m_dq_2rc v4 as having failed jobs 470s DEBUG  toil.leader:leader.py:1846 Cleaning the predecessors of kind-EncapsulatedJob/instance-sxnjxw3q 470s DEBUG  toil.toilState:toilState.py:283 Successors: one fewer for kind-_writer/instance-m_dq_2rc, now have 0 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-m_dq_2rc', result_status=0) 470s WARNING  toil.leader:leader.py:643 Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8 is completely failed 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:45:18: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:45:18: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 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. 470s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-m_dq_2rc v4 with result status: 0 470s DEBUG  toil.leader:leader.py:597 Job kind-_writer/instance-m_dq_2rc is being processed as completely failed 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_writer', job_id='kind-_writer/instance-m_dq_2rc') 470s DEBUG  toil.leader:leader.py:1735 Found new failed successors: of job: '_writer' kind-_writer/instance-m_dq_2rc v4 470s DEBUG  toil.leader:leader.py:969 Finished the main loop: no jobs left to run. 470s DEBUG  toil.serviceManager:serviceManager.py:236 Waiting for service manager thread to finish ... 470s DEBUG  toil.serviceManager:serviceManager.py:261 Received signal to quit starting services. 470s DEBUG  toil.serviceManager:serviceManager.py:243 ... finished shutting down the service manager. Took 1.2036736011505127 seconds 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:296 Waiting for stats and logging collator thread to finish ... 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:300 ... finished collating stats and logs. Took 0.0004417896270751953 seconds 470s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s INFO  toil.leader:leader.py:317 Finished toil run with 2 failed jobs. 470s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_writer' kind-_writer/instance-m_dq_2rc v4 '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8 470s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 470s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 470s DEBUG  toil.common:common.py:1800 Shutting down batch system ... 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:317 Daddy thread cleaning up 0 remaining children for batch system 130508088108624... 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:325 Daddy thread for batch system 130508088108624 finishing because no children should now exist 470s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:503 Attempting worker cleanup 470s DEBUG  toil.lib.threading:threading.py:109 Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s DEBUG  toil.deferred:deferred.py:215 Cleaning up deferred functions system 470s DEBUG  toil.deferred:deferred.py:159 Opened with own state file /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb/deferred/funczjvi3nd3 470s DEBUG  toil.deferred:deferred.py:291 Running orphaned deferred functions 470s DEBUG  toil.deferred:deferred.py:369 Ran orphaned deferred functions from 0 abandoned state files 470s DEBUG  toil.deferred:deferred.py:167 Removing own state file /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb/deferred/funczjvi3nd3 470s DEBUG  toil.lib.threading:threading.py:109 Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s DEBUG  toil.fileStores.cachingFileStore:cachingFileStore.py:2402 Connecting to latest caching database cache-0.db for cleanup 470s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:517 Deleting workflow directory /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/workdir/toilwf-87ccc014276c54d4ab5856eebd22a1fb 470s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:521 Deleting coordination directory /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb 470s DEBUG  toil.common:common.py:1802 ... finished shutting down the batch system in 0.01835036277770996 seconds. 470s INFO  toil.lib.history:history.py:530 Workflow 03001f5d-117e-4c91-9cbb-a0fb5b5551fd stopped. Success: False 470s __ TestSingleMachinePromisedRequirements.testPromisesWithNonCachingFileStore ___ 470s [gw2] linux -- Python 3.14.2 /usr/bin/python3.14 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 470s result: TResult | None = func() 470s ~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 470s lambda: runtest_hook(item=item, **kwds), 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 470s yield 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 470s return result.get_result() 470s ~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 470s raise exc.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 470s res = yield 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 470s teardown.throw(exception) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 470s return (yield) 470s ^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 470s item.runtest() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 470s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 470s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 470s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 470s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 470s raise exception 470s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 470s res = hook_impl.function(*args) 470s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 470s result = testfunction(**testargs) 470s File "/usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py", line 148, in testPromisesWithNonCachingFileStore 470s self.testPromisesWithJobStoreFileObjects(tmp_path, caching=False) 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py", line 145, in testPromisesWithJobStoreFileObjects 470s Job.Runner.startToil(F1, self.getOptions(tmp_path, caching=caching)) 470s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 470s return toil.start(job) 470s ~~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 470s return self._runMainLoop(rootJobDescription) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 470s ).run() 470s ~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 470s raise FailedJobsException( 470s ...<3 lines>... 470s ) 470s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore' contains 2 failed jobs: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8, '_writer' kind-_writer/instance-ufa6cd8w v4 470s Log from job "'_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8" follows: 470s =========> 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '54869bd2-945e-417d-912d-5a7984a4c75f', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp9l7ajwq8', '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} 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-76600b5057955753a6ab47b54c87702f/deferred/funcvyj00zir 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.worker] Parsed job description 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:25+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. 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:25+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. 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore'. 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6) from description '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:25+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 used 9.92x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s [2026-01-30T23:45:25+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 470s self.evaluatePromisedRequirements() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 470s ].getValue() 470s ~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 470s return func(*self._args) 470s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 470s 470s [2026-01-30T23:45:25+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [pydot] pydot initializing 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [pydot] pydot 4.0.1 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [pydot.core] pydot core module initializing 470s <========= 470s ----------------------------- Captured stderr call ----------------------------- 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.common] Initialized default configuration: {"config_version": 1.0} 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.batchSystems.options] Add options for aws_batch batch system 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.batchSystems.options] Add options for single_machine batch system 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.batchSystems.options] Add options for grid_engine batch system 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.batchSystems.options] Add options for lsf batch system 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.batchSystems.options] Add options for slurm batch system 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.batchSystems.options] Add options for torque batch system 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'test', 'cwltest', 'urllib3', 'docker', 'rdflib', 'humanfriendly', 'boto', 'asyncio', 'boto3', 'bcdocs', 'botocore', 'debugWorkflow', 'cachecontrol', 'concurrent', 'dill', 'requests', 'salad'} 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.statsAndLogging] Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'test', 'cwltest', 'urllib3', 'docker', 'rdflib', 'humanfriendly', 'boto', 'asyncio', 'boto3', 'bcdocs', 'botocore', 'debugWorkflow', 'cachecontrol', 'concurrent', 'dill', 'requests', 'salad'} 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.statsAndLogging] Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.common] Initialized default configuration: {"config_version": 1.0} 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.batchSystems.options] Add options for aws_batch batch system 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.batchSystems.options] Add options for single_machine batch system 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.batchSystems.options] Add options for grid_engine batch system 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.batchSystems.options] Add options for lsf batch system 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.batchSystems.options] Add options for slurm batch system 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.batchSystems.options] Add options for torque batch system 470s [2026-01-30T23:45:23+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-gw2/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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} 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore'. 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.jobStores.abstractJobStore] The workflow ID is: '54869bd2-945e-417d-912d-5a7984a4c75f' 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 54869bd2-945e-417d-912d-5a7984a4c75f in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.lib.history] Workflow 54869bd2-945e-417d-912d-5a7984a4c75f is a run of 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.common] Using the single machine batch system 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.common] Created the workflow directory for this machine at /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/workdir/toilwf-76600b5057955753a6ab47b54c87702f 470s [2026-01-30T23:45:23+0000] [Thread-80 (daddy)] [D] [toil.batchSystems.singleMachine] Started daddy thread for batch system 130508088112272. 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Started batch system 130508088112272 in normal mode. 470s [2026-01-30T23:45:23+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. 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.common] No user script to auto-deploy. 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.common] Written the environment for the jobs to the environment file 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.common] Caching all jobs in job store 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.common] 0 jobs downloaded. 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-7178243754fa4c2f8459765b29821e40/stream for result of '_writer' TemporaryID(52c05b7d-e1c1-4259-afb5-80f65739afe9) v0 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Saving graph of 5 jobs, 5 non-service, 5 new 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Processing job 'Job' kind-Job/instance-fps00snw v0 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Processing job '_follower' kind-_follower/instance-cltz3eg4 v0 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-a7e23f6052774bf1a7536d0008c364fa/stream for result of '_writer' kind-_writer/instance-ufa6cd8w v0 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-56d24525d3804848ad3acbf83618010b/stream for result of '_writer' kind-_writer/instance-1jw8a5fo v0 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v0 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-1jw8a5fo v0 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-ufa6cd8w v0 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] New job version: 'Job' kind-Job/instance-fps00snw v1 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-_follower/instance-cltz3eg4 v1 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-1jw8a5fo v1 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-ufa6cd8w v1 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '54869bd2-945e-417d-912d-5a7984a4c75f', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp9l7ajwq8', '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} 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.bus] Listening for message topic: toil.bus.JobUpdatedMessage 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.toilState] Found job to run: kind-_writer/instance-ufa6cd8w, with body: True, with checkpoint: False, with services: False, with no next successors: False 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-ufa6cd8w', result_status=0) 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.leader] Found 1 jobs to start and 0 jobs with successors to run 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.leader] Checked batch system has no running jobs and no updated jobs 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.serviceManager] Initializing service manager 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-ufa6cd8w v1 with result status: 0 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore kind-_writer/instance-ufa6cd8w with disk: 2.0 Gi, memory: 2.0 Gi, cores: 2.0, accelerators: [], preemptible: False 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.leader] Issued job '_writer' kind-_writer/instance-ufa6cd8w v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 2, accelerators: [], preemptible: False 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_writer', job_id='kind-_writer/instance-ufa6cd8w', toil_batch_id=1) 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 470s [2026-01-30T23:45:23+0000] [Thread-80 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore kind-_writer/instance-ufa6cd8w 470s [2026-01-30T23:45:23+0000] [Thread-80 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 1 as child 11850 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'boto3', 'requests', 'botocore', 'dill', 'concurrent', 'boto', 'urllib3', 'docker', 'asyncio'} 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.worker] Worker started for job _writer... 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.common] Obtained node ID d186161f45b648b99615a7187522b0d8 from file /var/lib/dbus/machine-id 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/workdir/toilwf-76600b5057955753a6ab47b54c87702f/dcb4/worker_log.txt 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-76600b5057955753a6ab47b54c87702f/deferred/func_50mwivr 470s [2026-01-30T23:45:24+0000] [Thread-83 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:45:24: Job '_writer' kind-_writer/instance-ufa6cd8w v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:24+0000] [Thread-83 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:45:24: Job '_writer' kind-_writer/instance-ufa6cd8w v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:24+0000] [Thread-83 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Received Toil worker log. Disable debug level logging to hide this output 470s [2026-01-30T23:45:24+0000] [Thread-83 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Log from job "JobFunctionWrappingJob" follows: 470s =========> 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '54869bd2-945e-417d-912d-5a7984a4c75f', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp9l7ajwq8', '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} 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-76600b5057955753a6ab47b54c87702f/deferred/func_50mwivr 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.worker] Parsed job description 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-ufa6cd8w v1 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:23+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. 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:23+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. 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-ufa6cd8w v1) from description '_writer' kind-_writer/instance-ufa6cd8w v1 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:23+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). 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-7178243754fa4c2f8459765b29821e40/stream from Job('_writer' kind-_writer/instance-ufa6cd8w v1) with a 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-a7e23f6052774bf1a7536d0008c364fa/stream from Job('_writer' kind-_writer/instance-ufa6cd8w v1) with a 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-ufa6cd8w v1 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-ufa6cd8w v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-ufa6cd8w v2 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-ufa6cd8w v2 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-ufa6cd8w v2 would chain to ID kind-_writer/instance-1jw8a5fo 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Chaining from '_writer' kind-_writer/instance-ufa6cd8w v2 to '_writer' kind-_writer/instance-1jw8a5fo v1 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] '_writer' kind-_writer/instance-1jw8a5fo v1 is adopting successor phases from '_writer' kind-_writer/instance-ufa6cd8w v2 of: [] 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-ufa6cd8w v3 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.worker] Starting the next job 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-ufa6cd8w v3 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-ufa6cd8w v3) from description '_writer' kind-_writer/instance-ufa6cd8w v3 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:23+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). 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-56d24525d3804848ad3acbf83618010b/stream from Job('_writer' kind-_writer/instance-ufa6cd8w v3) with a 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-ufa6cd8w v3 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-ufa6cd8w v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-ufa6cd8w v4 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-ufa6cd8w v4 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-ufa6cd8w v4 would chain to ID kind-EncapsulatedJob/instance-ppfmqql8 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.worker] Preemptibility is different for the next job, returning to the leader 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Not chaining from job '_writer' kind-_writer/instance-ufa6cd8w v4 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/workdir/toilwf-76600b5057955753a6ab47b54c87702f/dcb4. Set --cleanWorkDir to retain this log 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 0.199712 seconds 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [pydot] pydot initializing 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [pydot] pydot 4.0.1 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [pydot.core] pydot core module initializing 470s <========= 470s [2026-01-30T23:45:24+0000] [Thread-80 (daddy)] [D] [toil.batchSystems.singleMachine] Child 11850 for job 1 succeeded 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 1 with exit value: 0 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.leader] Job ended: '_writer' kind-_writer/instance-ufa6cd8w v1 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_writer', job_id='kind-_writer/instance-ufa6cd8w', exit_code=0) 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=1, external_batch_id='11850', batch_system='SingleMachineBatchSystem') 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.leader] Job '_writer' kind-_writer/instance-ufa6cd8w v1 continues to exist (i.e. has more to do) 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-ufa6cd8w', result_status=0) 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.leader] Added job: '_writer' kind-_writer/instance-ufa6cd8w v4 to updated jobs 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-ufa6cd8w v4 with result status: 0 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.leader] Job: kind-_writer/instance-ufa6cd8w has 1 successors to schedule 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.toilState] Successors: 1 more for kind-_writer/instance-ufa6cd8w, now have 1 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.leader] Added job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 as coming after job '_writer' kind-_writer/instance-ufa6cd8w v4 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-ppfmqql8 with disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.leader] Issued job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 with job batch system ID: 2 and disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-ppfmqql8', toil_batch_id=2) 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 470s [2026-01-30T23:45:24+0000] [Thread-80 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-ppfmqql8 470s [2026-01-30T23:45:24+0000] [Thread-80 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 2 as child 11994 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'botocore', 'urllib3', 'boto', 'dill', 'asyncio', 'requests', 'docker', 'boto3', 'concurrent'} 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.worker] Worker started for job EncapsulatedJob... 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.common] Obtained node ID d186161f45b648b99615a7187522b0d8 from file /var/lib/dbus/machine-id 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/workdir/toilwf-76600b5057955753a6ab47b54c87702f/7134/worker_log.txt 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v4 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-76600b5057955753a6ab47b54c87702f/deferred/funcz_bijkr6 470s [2026-01-30T23:45:24+0000] [Thread-80 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-ppfmqql8. 470s [2026-01-30T23:45:24+0000] [Thread-80 (daddy)] [D] [toil.batchSystems.singleMachine] Child 11994 for job 2 succeeded 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 2 with exit value: 1 470s [2026-01-30T23:45:24+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 470s Exit reason: None 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-ppfmqql8', exit_code=1) 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=2, external_batch_id='11994', batch_system='SingleMachineBatchSystem') 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.leader] Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 continues to exist (i.e. has more to do) 470s [2026-01-30T23:45:24+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v4 470s [2026-01-30T23:45:24+0000] [MainThread] [W] [toil.leader] Log from job "kind-EncapsulatedJob/instance-ppfmqql8" follows: 470s =========> 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '54869bd2-945e-417d-912d-5a7984a4c75f', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp9l7ajwq8', '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} 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-76600b5057955753a6ab47b54c87702f/deferred/funcz_bijkr6 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.worker] Parsed job description 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] Working on job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:24+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. 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:24+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. 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] Loaded body Job('EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1) from description 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Ran orphaned defE: pybuild pybuild:483: test: plugin pyproject failed with: exit code=1: cd /tmp/autopkgtest.IiScC1/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 470s I: pybuild base:384: cd /tmp/autopkgtest.IiScC1/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 470s erred functions from 0 abandoned state files 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v2 470s [2026-01-30T23:45:24+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v2 used 5.08x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] Completed body for 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v2 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.worker] 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v2 would chain to ID kind-_follower/instance-cltz3eg4 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] Chaining from 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v2 to '_follower' kind-_follower/instance-cltz3eg4 v1 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] '_follower' kind-_follower/instance-cltz3eg4 v1 is adopting successor phases from 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v2 of: [{'kind-Job/instance-fps00snw'}] 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v3 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.worker] Starting the next job 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v3 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore'. 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-ppfmqql8 v3) from description '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v3 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:24+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v3 used 4.47x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s [2026-01-30T23:45:24+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 470s self.evaluatePromisedRequirements() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 470s ].getValue() 470s ~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 470s return func(*self._args) 470s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 470s 470s [2026-01-30T23:45:24+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [pydot] pydot initializing 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [pydot] pydot 4.0.1 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [pydot.core] pydot core module initializing 470s <========= 470s [2026-01-30T23:45:24+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v4 with ID kind-EncapsulatedJob/instance-ppfmqql8 to 1 470s [2026-01-30T23:45:24+0000] [MainThread] [W] [toil.job] We have increased the default memory of the failed job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v4 to 2147483648 bytes 470s [2026-01-30T23:45:24+0000] [MainThread] [W] [toil.job] We have increased the disk of the failed job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v4 to the default of 2147483648 bytes 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v5 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-ppfmqql8', result_status=1) 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.leader] Added job: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v5 to updated jobs 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.leader] Updating status of job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v5 with result status: 1 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-ppfmqql8 with disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.leader] Issued job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v5 with job batch system ID: 3 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-ppfmqql8', toil_batch_id=3) 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 470s [2026-01-30T23:45:24+0000] [Thread-80 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-ppfmqql8 470s [2026-01-30T23:45:24+0000] [Thread-80 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 3 as child 12036 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'urllib3', 'concurrent', 'boto3', 'boto', 'asyncio', 'requests', 'botocore', 'docker', 'dill'} 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.worker] Worker started for job _follower... 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.common] Obtained node ID d186161f45b648b99615a7187522b0d8 from file /var/lib/dbus/machine-id 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/workdir/toilwf-76600b5057955753a6ab47b54c87702f/676c/worker_log.txt 470s [2026-01-30T23:45:25+0000] [Thread-83 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:45:25: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 470s [2026-01-30T23:45:25+0000] [Thread-83 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:45:25: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v2 used 5.08x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s [2026-01-30T23:45:25+0000] [Thread-83 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:45:25: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 470s [2026-01-30T23:45:25+0000] [Thread-83 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:45:25: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v3 used 4.47x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v7 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-76600b5057955753a6ab47b54c87702f/deferred/funcvyj00zir 470s [2026-01-30T23:45:25+0000] [Thread-80 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-ppfmqql8. 470s [2026-01-30T23:45:25+0000] [Thread-80 (daddy)] [D] [toil.batchSystems.singleMachine] Child 12036 for job 3 succeeded 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 3 with exit value: 1 470s [2026-01-30T23:45:25+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v5 470s Exit reason: None 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-ppfmqql8', exit_code=1) 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=3, external_batch_id='12036', batch_system='SingleMachineBatchSystem') 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.leader] Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v5 continues to exist (i.e. has more to do) 470s [2026-01-30T23:45:25+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v7 470s [2026-01-30T23:45:25+0000] [MainThread] [W] [toil.leader] Log from job "kind-EncapsulatedJob/instance-ppfmqql8" follows: 470s =========> 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '54869bd2-945e-417d-912d-5a7984a4c75f', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp9l7ajwq8', '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} 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-76600b5057955753a6ab47b54c87702f/deferred/funcvyj00zir 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.worker] Parsed job description 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:25+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. 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:25+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. 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore'. 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6) from description '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:25+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 used 9.92x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s [2026-01-30T23:45:25+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 470s self.evaluatePromisedRequirements() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 470s ].getValue() 470s ~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 470s return func(*self._args) 470s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 470s 470s [2026-01-30T23:45:25+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [pydot] pydot initializing 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [pydot] pydot 4.0.1 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [pydot.core] pydot core module initializing 470s <========= 470s [2026-01-30T23:45:25+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v7 with ID kind-EncapsulatedJob/instance-ppfmqql8 to 0 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-ppfmqql8', result_status=1) 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.leader] Added job: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8 to updated jobs 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.leader] Updating status of job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8 with result status: 1 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-ppfmqql8') 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.leader] Found new failed successors: kind-Job/instance-fps00snw of job: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.leader] Totally failed job: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8 is marking direct predecessor: '_writer' kind-_writer/instance-ufa6cd8w v4 as having failed jobs 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.leader] Cleaning the predecessors of kind-EncapsulatedJob/instance-ppfmqql8 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.toilState] Successors: one fewer for kind-_writer/instance-ufa6cd8w, now have 0 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-ufa6cd8w', result_status=0) 470s [2026-01-30T23:45:25+0000] [MainThread] [W] [toil.leader] Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8 is completely failed 470s [2026-01-30T23:45:25+0000] [Thread-83 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:45:25: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:25+0000] [Thread-83 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:45:25: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 used 9.92x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s [2026-01-30T23:45:27+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s [2026-01-30T23:45:27+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-ufa6cd8w v4 with result status: 0 470s [2026-01-30T23:45:27+0000] [MainThread] [D] [toil.leader] Job kind-_writer/instance-ufa6cd8w is being processed as completely failed 470s [2026-01-30T23:45:27+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_writer', job_id='kind-_writer/instance-ufa6cd8w') 470s [2026-01-30T23:45:27+0000] [MainThread] [D] [toil.leader] Found new failed successors: of job: '_writer' kind-_writer/instance-ufa6cd8w v4 470s [2026-01-30T23:45:29+0000] [MainThread] [D] [toil.leader] Finished the main loop: no jobs left to run. 470s [2026-01-30T23:45:29+0000] [MainThread] [D] [toil.serviceManager] Waiting for service manager thread to finish ... 470s [2026-01-30T23:45:29+0000] [Thread-82 (__start_services)] [D] [toil.serviceManager] Received signal to quit starting services. 470s [2026-01-30T23:45:30+0000] [MainThread] [D] [toil.serviceManager] ... finished shutting down the service manager. Took 1.224909782409668 seconds 470s [2026-01-30T23:45:30+0000] [MainThread] [D] [toil.statsAndLogging] Waiting for stats and logging collator thread to finish ... 470s [2026-01-30T23:45:30+0000] [MainThread] [D] [toil.statsAndLogging] ... finished collating stats and logs. Took 0.007964611053466797 seconds 470s [2026-01-30T23:45:30+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s [2026-01-30T23:45:30+0000] [MainThread] [I] [toil.leader] Finished toil run with 2 failed jobs. 470s [2026-01-30T23:45:30+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8 '_writer' kind-_writer/instance-ufa6cd8w v4 470s [2026-01-30T23:45:30+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 470s [2026-01-30T23:45:31+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 470s [2026-01-30T23:45:31+0000] [MainThread] [D] [toil.common] Shutting down batch system ... 470s [2026-01-30T23:45:31+0000] [Thread-80 (daddy)] [D] [toil.batchSystems.singleMachine] Daddy thread cleaning up 0 remaining children for batch system 130508088112272... 470s [2026-01-30T23:45:31+0000] [Thread-80 (daddy)] [D] [toil.batchSystems.singleMachine] Daddy thread for batch system 130508088112272 finishing because no children should now exist 470s [2026-01-30T23:45:31+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Attempting worker cleanup 470s [2026-01-30T23:45:31+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:31+0000] [MainThread] [D] [toil.deferred] Cleaning up deferred functions system 470s [2026-01-30T23:45:31+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-76600b5057955753a6ab47b54c87702f/deferred/funck7k96w_f 470s [2026-01-30T23:45:31+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:31+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:31+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-76600b5057955753a6ab47b54c87702f/deferred/funck7k96w_f 470s [2026-01-30T23:45:31+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:31+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Deleting workflow directory /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/workdir/toilwf-76600b5057955753a6ab47b54c87702f 470s [2026-01-30T23:45:31+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Deleting coordination directory /run/lock/toilwf-76600b5057955753a6ab47b54c87702f 470s [2026-01-30T23:45:31+0000] [MainThread] [D] [toil.common] ... finished shutting down the batch system in 0.01809239387512207 seconds. 470s [2026-01-30T23:45:31+0000] [MainThread] [I] [toil.lib.history] Workflow 54869bd2-945e-417d-912d-5a7984a4c75f stopped. Success: False 470s ------------------------------ Captured log call ------------------------------- 470s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s DEBUG  toil.common:common.py:796 Initialized default configuration: {"config_version": 1.0} 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for aws_batch batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for single_machine batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for grid_engine batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for lsf batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for slurm batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for torque batch system 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:488 Suppressing the following loggers: {'test', 'cwltest', 'urllib3', 'docker', 'rdflib', 'humanfriendly', 'boto', 'asyncio', 'boto3', 'bcdocs', 'botocore', 'debugWorkflow', 'cachecontrol', 'concurrent', 'dill', 'requests', 'salad'} 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:447 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:488 Suppressing the following loggers: {'test', 'cwltest', 'urllib3', 'docker', 'rdflib', 'humanfriendly', 'boto', 'asyncio', 'boto3', 'bcdocs', 'botocore', 'debugWorkflow', 'cachecontrol', 'concurrent', 'dill', 'requests', 'salad'} 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:447 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 470s DEBUG  toil.common:common.py:796 Initialized default configuration: {"config_version": 1.0} 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for aws_batch batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for single_machine batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for grid_engine batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for lsf batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for slurm batch system 470s DEBUG  toil.batchSystems.options:options.py:207 Add options for torque batch system 470s 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-gw2/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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} 470s DEBUG  toil.jobStores.fileJobStore:fileJobStore.py:93 Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore'. 470s DEBUG  toil.jobStores.abstractJobStore:abstractJobStore.py:212 The workflow ID is: '54869bd2-945e-417d-912d-5a7984a4c75f' 470s INFO  toil.lib.history:history.py:369 Recording workflow creation of 54869bd2-945e-417d-912d-5a7984a4c75f in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore 470s INFO  toil.lib.history:history.py:399 Workflow 54869bd2-945e-417d-912d-5a7984a4c75f is a run of 470s DEBUG  toil.common:common.py:1346 Using the single machine batch system 470s DEBUG  toil.common:common.py:1723 Created the workflow directory for this machine at /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/workdir/toilwf-76600b5057955753a6ab47b54c87702f 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:247 Started daddy thread for batch system 130508088112272. 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:229 Started batch system 130508088112272 in normal mode. 470s 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. 470s DEBUG  toil.common:common.py:1409 No user script to auto-deploy. 470s DEBUG  toil.common:common.py:1576 Written the environment for the jobs to the environment file 470s DEBUG  toil.common:common.py:1580 Caching all jobs in job store 470s DEBUG  toil.common:common.py:1584 0 jobs downloaded. 470s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-7178243754fa4c2f8459765b29821e40/stream for result of '_writer' TemporaryID(52c05b7d-e1c1-4259-afb5-80f65739afe9) v0 470s DEBUG  toil.job:job.py:3000 Saving graph of 5 jobs, 5 non-service, 5 new 470s DEBUG  toil.job:job.py:3023 Processing job 'Job' kind-Job/instance-fps00snw v0 470s DEBUG  toil.job:job.py:3023 Processing job '_follower' kind-_follower/instance-cltz3eg4 v0 470s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-a7e23f6052774bf1a7536d0008c364fa/stream for result of '_writer' kind-_writer/instance-ufa6cd8w v0 470s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-56d24525d3804848ad3acbf83618010b/stream for result of '_writer' kind-_writer/instance-1jw8a5fo v0 470s DEBUG  toil.job:job.py:3023 Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v0 470s DEBUG  toil.job:job.py:3023 Processing job '_writer' kind-_writer/instance-1jw8a5fo v0 470s DEBUG  toil.job:job.py:3023 Processing job '_writer' kind-_writer/instance-ufa6cd8w v0 470s DEBUG  toil.job:job.py:1507 New job version: 'Job' kind-Job/instance-fps00snw v1 470s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-_follower/instance-cltz3eg4 v1 470s DEBUG  toil.job:job.py:1507 New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 470s DEBUG  toil.job:job.py:1507 New job version: '_writer' kind-_writer/instance-1jw8a5fo v1 470s DEBUG  toil.job:job.py:1507 New job version: '_writer' kind-_writer/instance-ufa6cd8w v1 470s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s DEBUG  toil:__init__.py:481 Configuration: {'cwl': False, 'workflowID': '54869bd2-945e-417d-912d-5a7984a4c75f', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp9l7ajwq8', '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} 470s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 470s DEBUG  toil.bus:bus.py:403 Listening for message topic: toil.bus.JobUpdatedMessage 470s DEBUG  toil.toilState:toilState.py:322 Found job to run: kind-_writer/instance-ufa6cd8w, with body: True, with checkpoint: False, with services: False, with no next successors: False 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-ufa6cd8w', result_status=0) 470s DEBUG  toil.leader:leader.py:145 Found 1 jobs to start and 0 jobs with successors to run 470s DEBUG  toil.leader:leader.py:157 Checked batch system has no running jobs and no updated jobs 470s DEBUG  toil.serviceManager:serviceManager.py:35 Initializing service manager 470s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-ufa6cd8w v1 with result status: 0 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore kind-_writer/instance-ufa6cd8w with disk: 2.0 Gi, memory: 2.0 Gi, cores: 2.0, accelerators: [], preemptible: False 470s INFO  toil.leader:leader.py:1132 Issued job '_writer' kind-_writer/instance-ufa6cd8w v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 2, accelerators: [], preemptible: False 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_writer', job_id='kind-_writer/instance-ufa6cd8w', toil_batch_id=1) 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore kind-_writer/instance-ufa6cd8w 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 1 as child 11850 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:45:24: Job '_writer' kind-_writer/instance-ufa6cd8w v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:45:24: Job '_writer' kind-_writer/instance-ufa6cd8w v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:98 Received Toil worker log. Disable debug level logging to hide this output 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:101 Log from job "JobFunctionWrappingJob" follows: 470s =========> 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '54869bd2-945e-417d-912d-5a7984a4c75f', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp9l7ajwq8', '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} 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-76600b5057955753a6ab47b54c87702f/deferred/func_50mwivr 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.worker] Parsed job description 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-ufa6cd8w v1 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:23+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. 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:23+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. 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-ufa6cd8w v1) from description '_writer' kind-_writer/instance-ufa6cd8w v1 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:23+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). 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-7178243754fa4c2f8459765b29821e40/stream from Job('_writer' kind-_writer/instance-ufa6cd8w v1) with a 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-a7e23f6052774bf1a7536d0008c364fa/stream from Job('_writer' kind-_writer/instance-ufa6cd8w v1) with a 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-ufa6cd8w v1 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-ufa6cd8w v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-ufa6cd8w v2 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-ufa6cd8w v2 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-ufa6cd8w v2 would chain to ID kind-_writer/instance-1jw8a5fo 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Chaining from '_writer' kind-_writer/instance-ufa6cd8w v2 to '_writer' kind-_writer/instance-1jw8a5fo v1 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] '_writer' kind-_writer/instance-1jw8a5fo v1 is adopting successor phases from '_writer' kind-_writer/instance-ufa6cd8w v2 of: [] 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-ufa6cd8w v3 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.worker] Starting the next job 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-ufa6cd8w v3 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-ufa6cd8w v3) from description '_writer' kind-_writer/instance-ufa6cd8w v3 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:23+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). 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-56d24525d3804848ad3acbf83618010b/stream from Job('_writer' kind-_writer/instance-ufa6cd8w v3) with a 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-ufa6cd8w v3 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-ufa6cd8w v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-ufa6cd8w v4 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-ufa6cd8w v4 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-ufa6cd8w v4 would chain to ID kind-EncapsulatedJob/instance-ppfmqql8 470s [2026-01-30T23:45:23+0000] [MainThread] [D] [toil.worker] Preemptibility is different for the next job, returning to the leader 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Not chaining from job '_writer' kind-_writer/instance-ufa6cd8w v4 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/workdir/toilwf-76600b5057955753a6ab47b54c87702f/dcb4. Set --cleanWorkDir to retain this log 470s [2026-01-30T23:45:23+0000] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 0.199712 seconds 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [pydot] pydot initializing 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [pydot] pydot 4.0.1 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [pydot.core] pydot core module initializing 470s <========= 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 11850 for job 1 succeeded 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 1 with exit value: 0 470s DEBUG  toil.leader:leader.py:846 Job ended: '_writer' kind-_writer/instance-ufa6cd8w v1 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_writer', job_id='kind-_writer/instance-ufa6cd8w', exit_code=0) 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=1, external_batch_id='11850', batch_system='SingleMachineBatchSystem') 470s DEBUG  toil.leader:leader.py:1455 Job '_writer' kind-_writer/instance-ufa6cd8w v1 continues to exist (i.e. has more to do) 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-ufa6cd8w', result_status=0) 470s DEBUG  toil.leader:leader.py:1620 Added job: '_writer' kind-_writer/instance-ufa6cd8w v4 to updated jobs 470s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 470s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-ufa6cd8w v4 with result status: 0 470s DEBUG  toil.leader:leader.py:506 Job: kind-_writer/instance-ufa6cd8w has 1 successors to schedule 470s DEBUG  toil.toilState:toilState.py:264 Successors: 1 more for kind-_writer/instance-ufa6cd8w, now have 1 470s DEBUG  toil.leader:leader.py:476 Added job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 as coming after job '_writer' kind-_writer/instance-ufa6cd8w v4 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-ppfmqql8 with disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 470s INFO  toil.leader:leader.py:1132 Issued job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 with job batch system ID: 2 and disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-ppfmqql8', toil_batch_id=2) 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-ppfmqql8 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 2 as child 11994 470s 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-gw2/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-ppfmqql8. 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 11994 for job 2 succeeded 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 2 with exit value: 1 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 470s Exit reason: None 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-ppfmqql8', exit_code=1) 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=2, external_batch_id='11994', batch_system='SingleMachineBatchSystem') 470s DEBUG  toil.leader:leader.py:1455 Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 continues to exist (i.e. has more to do) 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v4 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-EncapsulatedJob/instance-ppfmqql8" follows: 470s =========> 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '54869bd2-945e-417d-912d-5a7984a4c75f', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp9l7ajwq8', '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} 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-76600b5057955753a6ab47b54c87702f/deferred/funcz_bijkr6 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.worker] Parsed job description 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] Working on job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:24+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. 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:24+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. 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] Loaded body Job('EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1) from description 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v2 470s [2026-01-30T23:45:24+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v2 used 5.08x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] Completed body for 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v2 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.worker] 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v2 would chain to ID kind-_follower/instance-cltz3eg4 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] Chaining from 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v2 to '_follower' kind-_follower/instance-cltz3eg4 v1 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] '_follower' kind-_follower/instance-cltz3eg4 v1 is adopting successor phases from 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v2 of: [{'kind-Job/instance-fps00snw'}] 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v3 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.worker] Starting the next job 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v3 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore'. 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-ppfmqql8 v3) from description '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v3 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:24+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v3 used 4.47x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s [2026-01-30T23:45:24+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 470s self.evaluatePromisedRequirements() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 470s ].getValue() 470s ~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 470s return func(*self._args) 470s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 470s 470s [2026-01-30T23:45:24+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [pydot] pydot initializing 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [pydot] pydot 4.0.1 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [pydot.core] pydot core module initializing 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v4 with ID kind-EncapsulatedJob/instance-ppfmqql8 to 1 470s WARNING  toil.job:job.py:1413 We have increased the default memory of the failed job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v4 to 2147483648 bytes 470s WARNING  toil.job:job.py:1421 We have increased the disk of the failed job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v4 to the default of 2147483648 bytes 470s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v5 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-ppfmqql8', result_status=1) 470s DEBUG  toil.leader:leader.py:1620 Added job: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v5 to updated jobs 470s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s DEBUG  toil.leader:leader.py:606 Updating status of job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v5 with result status: 1 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-ppfmqql8 with disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 470s INFO  toil.leader:leader.py:1132 Issued job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v5 with job batch system ID: 3 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-ppfmqql8', toil_batch_id=3) 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-ppfmqql8 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 3 as child 12036 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:45:25: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:45:25: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-ppfmqql8 v2 used 5.08x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:45:25: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:45:25: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v3 used 4.47x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s 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-gw2/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-ppfmqql8. 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 12036 for job 3 succeeded 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 3 with exit value: 1 470s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v5 470s Exit reason: None 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-ppfmqql8', exit_code=1) 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=3, external_batch_id='12036', batch_system='SingleMachineBatchSystem') 470s DEBUG  toil.leader:leader.py:1455 Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v5 continues to exist (i.e. has more to do) 470s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v7 470s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-EncapsulatedJob/instance-ppfmqql8" follows: 470s =========> 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '54869bd2-945e-417d-912d-5a7984a4c75f', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp9l7ajwq8', '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} 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-76600b5057955753a6ab47b54c87702f/deferred/funcvyj00zir 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.worker] Parsed job description 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:25+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. 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:25+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. 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore'. 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6) from description '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:25+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 used 9.92x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s [2026-01-30T23:45:25+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 470s self.evaluatePromisedRequirements() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 470s ].getValue() 470s ~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 470s return func(*self._args) 470s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 470s 470s [2026-01-30T23:45:25+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [pydot] pydot initializing 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [pydot] pydot 4.0.1 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [pydot.core] pydot core module initializing 470s <========= 470s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v7 with ID kind-EncapsulatedJob/instance-ppfmqql8 to 0 470s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-ppfmqql8', result_status=1) 470s DEBUG  toil.leader:leader.py:1620 Added job: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8 to updated jobs 470s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s DEBUG  toil.leader:leader.py:606 Updating status of job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8 with result status: 1 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-ppfmqql8') 470s DEBUG  toil.leader:leader.py:1735 Found new failed successors: kind-Job/instance-fps00snw of job: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8 470s DEBUG  toil.leader:leader.py:1779 Totally failed job: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8 is marking direct predecessor: '_writer' kind-_writer/instance-ufa6cd8w v4 as having failed jobs 470s DEBUG  toil.leader:leader.py:1846 Cleaning the predecessors of kind-EncapsulatedJob/instance-ppfmqql8 470s DEBUG  toil.toilState:toilState.py:283 Successors: one fewer for kind-_writer/instance-ufa6cd8w, now have 0 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-ufa6cd8w', result_status=0) 470s WARNING  toil.leader:leader.py:643 Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8 is completely failed 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:45:25: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 470s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:45:25: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 used 9.92x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 470s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-ufa6cd8w v4 with result status: 0 470s DEBUG  toil.leader:leader.py:597 Job kind-_writer/instance-ufa6cd8w is being processed as completely failed 470s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_writer', job_id='kind-_writer/instance-ufa6cd8w') 470s DEBUG  toil.leader:leader.py:1735 Found new failed successors: of job: '_writer' kind-_writer/instance-ufa6cd8w v4 470s DEBUG  toil.leader:leader.py:969 Finished the main loop: no jobs left to run. 470s DEBUG  toil.serviceManager:serviceManager.py:236 Waiting for service manager thread to finish ... 470s DEBUG  toil.serviceManager:serviceManager.py:261 Received signal to quit starting services. 470s DEBUG  toil.serviceManager:serviceManager.py:243 ... finished shutting down the service manager. Took 1.224909782409668 seconds 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:296 Waiting for stats and logging collator thread to finish ... 470s DEBUG  toil.statsAndLogging:statsAndLogging.py:300 ... finished collating stats and logs. Took 0.007964611053466797 seconds 470s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s INFO  toil.leader:leader.py:317 Finished toil run with 2 failed jobs. 470s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8 '_writer' kind-_writer/instance-ufa6cd8w v4 470s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 470s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 470s DEBUG  toil.common:common.py:1800 Shutting down batch system ... 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:317 Daddy thread cleaning up 0 remaining children for batch system 130508088112272... 470s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:325 Daddy thread for batch system 130508088112272 finishing because no children should now exist 470s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:503 Attempting worker cleanup 470s DEBUG  toil.lib.threading:threading.py:109 Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s DEBUG  toil.deferred:deferred.py:215 Cleaning up deferred functions system 470s DEBUG  toil.deferred:deferred.py:159 Opened with own state file /run/lock/toilwf-76600b5057955753a6ab47b54c87702f/deferred/funck7k96w_f 470s DEBUG  toil.deferred:deferred.py:291 Running orphaned deferred functions 470s DEBUG  toil.deferred:deferred.py:369 Ran orphaned deferred functions from 0 abandoned state files 470s DEBUG  toil.deferred:deferred.py:167 Removing own state file /run/lock/toilwf-76600b5057955753a6ab47b54c87702f/deferred/funck7k96w_f 470s DEBUG  toil.lib.threading:threading.py:109 Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:517 Deleting workflow directory /tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/workdir/toilwf-76600b5057955753a6ab47b54c87702f 470s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:521 Deleting coordination directory /run/lock/toilwf-76600b5057955753a6ab47b54c87702f 470s DEBUG  toil.common:common.py:1802 ... finished shutting down the batch system in 0.01809239387512207 seconds. 470s INFO  toil.lib.history:history.py:530 Workflow 54869bd2-945e-417d-912d-5a7984a4c75f stopped. Success: False 470s =========================== short test summary info ============================ 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:603: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:217: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:189: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1115: Configure AWS credentials to include this test. 470s 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. 470s 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. 470s 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. 470s 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. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1127: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:621: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:825: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:800: Configure AWS credentials to include this test. 470s 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. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:151: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:160: Configure AWS credentials to include this test. 470s 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. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:313: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:202: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1467: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1446: Configure AWS credentials to include this test. 470s 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. 470s 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. 470s 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. 470s 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. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1079: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:450: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:238: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:421: Configure AWS credentials to include this test. 470s 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. 470s 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. 470s 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. 470s 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. 470s 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. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:405: Configure AWS credentials to include this test. 470s 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. 470s 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. 470s 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. 470s 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. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:380: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:529: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:264: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:585: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:960: Configure AWS credentials to include this test. 470s SKIPPED [13] ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py:1139: Configure AWS credentials to include this test. 470s 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. 470s 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. 470s 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. 470s 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. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:32: Consumes unauthenticated Docker Hub pulls if run 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:38: Consumes unauthenticated Docker Hub pulls if run 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:45: Consumes unauthenticated Docker Hub pulls if run 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:26: Consumes unauthenticated Docker Hub pulls if run 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:731: Install Toil with the 'server' extra to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:646: Install Toil with the 'server' extra to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:697: Install Toil with the 'server' extra to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:706: Install Toil with the 'server' extra to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:685: Install Toil with the 'server' extra to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:676: Install Toil with the 'server' extra to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:721: Install Toil with the 'server' extra to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:619: Install Toil with the 'server' extra to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:600: Install Toil with the 'server' extra to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:668: Install Toil with the 'server' extra to include this test. 470s 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. 470s 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. 470s 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. 470s 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. 470s 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. 470s 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. 470s 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. 470s 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. 470s 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. 470s 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. 470s SKIPPED [7] ../../../../usr/lib/python3/dist-packages/_pytest/unittest.py:498: Configure AWS credentials to include this test. 470s 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. 470s 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. 470s 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. 470s 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. 470s 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. 470s 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. 470s 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. 470s 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. 470s 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. 470s 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. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:541: Install Toil with the 'server' extra to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:535: Install Toil with the 'server' extra to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:526: Install Toil with the 'server' extra to include this test. 470s 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. 470s 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. 470s 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. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py:255: Install Toil with the 'wdl' extra to include this test. 470s SKIPPED [3] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:96: Install Toil with the 'server' extra to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:245: Install Toil with the 'server' extra to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1568: Configure AWS credentials to include this test. 470s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:48: Install Toil with the 'server' extra to include this test. 470s 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' 470s FAILED docs/scriptsTest.py::ToilDocumentationTest::testDocker - RuntimeError: [2026-01-30T23:42:35+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 2fc1ff03-68c0-4019-b651-8a1c66d3aaca in file:/tmp/tmpgtxpsj66tutorial_docker 470s [2026-01-30T23:42:35+0000] [MainThread] [I] [toil.lib.history] Workflow 2fc1ff03-68c0-4019-b651-8a1c66d3aaca is a run of /usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py 470s [2026-01-30T23:42:35+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:35+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 470s [2026-01-30T23:42:35+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:42:36+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmpgtxpsj66tutorial_docker kind-apiDockerCall/instance-jkwrggqq. 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v1 470s Exit reason: None 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v2 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-jkwrggqq" follows: 470s =========> 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v1 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v1) from description 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v1 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq 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. 470s [2026-01-30T23:42:36+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:36+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v2 with ID kind-apiDockerCall/instance-jkwrggqq to 1 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 470s [2026-01-30T23:42:36+0000] [Thread-4 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:42:36: Job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq 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. 470s [2026-01-30T23:42:36+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmpgtxpsj66tutorial_docker kind-apiDockerCall/instance-jkwrggqq. 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v3 470s Exit reason: None 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v5 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-jkwrggqq" follows: 470s =========> 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v4 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v4) from description 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v4 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq 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. 470s [2026-01-30T23:42:36+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:36+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v5 with ID kind-apiDockerCall/instance-jkwrggqq to 0 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.leader] Job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v6 is completely failed 470s [2026-01-30T23:42:36+0000] [Thread-4 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:42:36: Job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq 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. 470s [2026-01-30T23:42:39+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 470s [2026-01-30T23:42:39+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 470s [2026-01-30T23:42:39+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v6 470s [2026-01-30T23:42:39+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 470s [2026-01-30T23:42:40+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 470s [2026-01-30T23:42:40+0000] [MainThread] [I] [toil.lib.history] Workflow 2fc1ff03-68c0-4019-b651-8a1c66d3aaca stopped. Success: False 470s [2026-01-30T23:42:40+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/tmpgtxpsj66tutorial_docker) 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py", line 20, in 470s toil.start(align) 470s ~~~~~~~~~~^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 470s return self._runMainLoop(rootJobDescription) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 470s ).run() 470s ~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 470s raise FailedJobsException( 470s ...<3 lines>... 470s ) 470s toil.exceptions.FailedJobsException: The job store '/tmp/tmpgtxpsj66tutorial_docker' contains 1 failed jobs: 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v6 470s Log from job "'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v6" follows: 470s =========> 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v4 470s [2026-01-30T23:42:36+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v4) from description 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq v4 470s [2026-01-30T23:42:36+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-jkwrggqq 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. 470s [2026-01-30T23:42:36+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:36+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s 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' 470s 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' 470s 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' 470s 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-8mvo8au_ v6 470s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v6" follows: 470s =========> 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v4 470s [2026-01-30T23:42:51+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ v4 470s [2026-01-30T23:42:51+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-8mvo8au_ 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. 470s [2026-01-30T23:42:51+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 470s return apiDockerCall( 470s job, 470s ...<2 lines>... 470s privileged=True, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:51+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s 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-vvxmcars v6 470s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v6" follows: 470s =========> 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v4 470s [2026-01-30T23:42:56+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars v4 470s [2026-01-30T23:42:56+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-vvxmcars 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. 470s [2026-01-30T23:42:56+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 470s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 470s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:42:56+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s 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-blbzi76y v6 470s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v6" follows: 470s =========> 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v4 470s [2026-01-30T23:43:00+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y v4 470s [2026-01-30T23:43:00+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-blbzi76y 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. 470s [2026-01-30T23:43:00+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 470s return apiDockerCall( 470s job, 470s ...<2 lines>... 470s privileged=True, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:00+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s 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-pfq3h7nz v6 470s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v6" follows: 470s =========> 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v4 470s [2026-01-30T23:43:04+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz v4 470s [2026-01-30T23:43:05+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-pfq3h7nz 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. 470s [2026-01-30T23:43:05+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 470s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 470s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:05+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s 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-iytpr4c6 v6 470s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v6" follows: 470s =========> 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v4 470s [2026-01-30T23:43:11+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 v4 470s [2026-01-30T23:43:11+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-iytpr4c6 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. 470s [2026-01-30T23:43:11+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:11+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s 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-3rqvtl5u v6 470s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v6" follows: 470s =========> 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v4 470s [2026-01-30T23:43:17+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u v4 470s [2026-01-30T23:43:17+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-3rqvtl5u 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. 470s [2026-01-30T23:43:17+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:17+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s 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-0qs6m4d8 v6 470s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v6" follows: 470s =========> 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:21+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v4 470s [2026-01-30T23:43:22+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 v4 470s [2026-01-30T23:43:22+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-0qs6m4d8 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. 470s [2026-01-30T23:43:22+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:22+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s 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-i80eael6 v6 470s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v6" follows: 470s =========> 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:43:25+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v4 470s [2026-01-30T23:43:26+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 v4 470s [2026-01-30T23:43:26+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-i80eael6 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. 470s [2026-01-30T23:43:26+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s PermissionError: [Errno 13] Permission denied 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 470s resp = conn.urlopen( 470s method=request.method, 470s ...<9 lines>... 470s chunked=chunked, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 470s retries = retries.increment( 470s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 470s raise reraise(type(error), error, _stacktrace) 470s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 470s raise value.with_traceback(tb) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 470s response = self._make_request( 470s conn, 470s ...<10 lines>... 470s **response_kw, 470s ) 470s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 470s conn.request( 470s ~~~~~~~~~~~~^ 470s method, 470s ^^^^^^^ 470s ...<6 lines>... 470s enforce_content_length=enforce_content_length, 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 470s self.endheaders() 470s ~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 470s self._send_output(message_body, encode_chunked=encode_chunked) 470s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 470s self.send(msg) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3.13/http/client.py", line 1057, in send 470s self.connect() 470s ~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 470s sock.connect(self.unix_socket) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 470s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s During handling of the above exception, another exception occurred: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 470s return self.version(api_version=False)["ApiVersion"] 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 470s return self._result(self._get(url), json=True) 470s ~~~~~~~~~^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 470s return f(self, *args, **kwargs) 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 470s return self.get(url, **self._set_request_timeout(kwargs)) 470s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 470s return self.request("GET", url, **kwargs) 470s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 470s resp = self.send(prep, **send_kwargs) 470s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 470s r = adapter.send(request, **kwargs) 470s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 470s raise ConnectionError(err, request=request) 470s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s The above exception was the direct cause of the following exception: 470s 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 470s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 470s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 470s out = apiDockerCall( 470s job, 470s ...<8 lines>... 470s demux=demux, 470s ) 470s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 470s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 470s return cls( 470s timeout=timeout, 470s ...<3 lines>... 470s **kwargs_from_env(**kwargs) 470s ) 470s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 470s self.api = APIClient(*args, **kwargs) 470s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 470s self._version = self._retrieve_server_version() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 470s raise DockerException( 470s f'Error while fetching server API version: {e}' 470s ) from e 470s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 470s 470s [2026-01-30T23:43:26+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s <========= 470s FAILED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithJobStoreFileObjects - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore' contains 2 failed jobs: '_writer' kind-_writer/instance-m_dq_2rc v4, '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8 470s Log from job "'_follower' kind-EncapsulatedJob/instance-sxnjxw3q v8" follows: 470s =========> 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '03001f5d-117e-4c91-9cbb-a0fb5b5551fd', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp2uq1k373', '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} 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb/deferred/funcqfazzvrg 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.worker] Parsed job description 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 470s [2026-01-30T23:45:17+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 470s [2026-01-30T23:45:17+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:18+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. 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:18+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. 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithJobStoreFileOb0/jobstore'. 470s [2026-01-30T23:45:18+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6) from description '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-87ccc014276c54d4ab5856eebd22a1fb has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6) with ID (kind-EncapsulatedJob/instance-sxnjxw3q). 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6) with ID (kind-EncapsulatedJob/instance-sxnjxw3q) which wants 2147483648 of our 98496815104 bytes. 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 98496815104 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 98496815104 bytes 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:18+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-sxnjxw3q v6 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. 470s [2026-01-30T23:45:18+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 470s self.evaluatePromisedRequirements() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 470s ].getValue() 470s ~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 470s return func(*self._args) 470s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 470s 470s [2026-01-30T23:45:18+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [pydot] pydot initializing 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [pydot] pydot 4.0.1 470s [2026-01-30T23:45:18+0000] [MainThread] [D] [pydot.core] pydot core module initializing 470s <========= 470s FAILED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithNonCachingFileStore - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore' contains 2 failed jobs: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8, '_writer' kind-_writer/instance-ufa6cd8w v4 470s Log from job "'_follower' kind-EncapsulatedJob/instance-ppfmqql8 v8" follows: 470s =========> 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '54869bd2-945e-417d-912d-5a7984a4c75f', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/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/tmp9l7ajwq8', '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} 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-76600b5057955753a6ab47b54c87702f/deferred/funcvyj00zir 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.worker] Parsed job description 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 470s [2026-01-30T23:45:24+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 470s [2026-01-30T23:45:24+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:25+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. 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 470s [2026-01-30T23:45:25+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. 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw2/testPromisesWithNonCachingFile0/jobstore'. 470s [2026-01-30T23:45:25+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6) from description '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-76600b5057955753a6ab47b54c87702f has lockable filesystem type: tmpfs 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Running job 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 470s [2026-01-30T23:45:25+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-ppfmqql8 v6 used 9.92x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 470s [2026-01-30T23:45:25+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 470s Traceback (most recent call last): 470s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 470s job._runner( 470s ~~~~~~~~~~~^ 470s jobGraph=None, 470s ^^^^^^^^^^^^^^ 470s ...<2 lines>... 470s defer=defer, 470s ^^^^^^^^^^^^ 470s ) 470s ^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 470s returnValues = self._run(jobGraph=None, fileStore=fileStore) 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 470s return self.run(fileStore) 470s ~~~~~~~~^^^^^^^^^^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 470s self.evaluatePromisedRequirements() 470s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 470s ].getValue() 470s ~~~~~~~~^^ 470s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 470s return func(*self._args) 470s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 470s 470s [2026-01-30T23:45:25+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [pydot] pydot initializing 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [pydot] pydot 4.0.1 470s [2026-01-30T23:45:25+0000] [MainThread] [D] [pydot.core] pydot core module initializing 470s <========= 470s ERROR src/importExportFileTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py'. 470s Hint: make sure your test modules/packages have valid Python names. 470s Traceback: 470s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 470s mod = import_path( 470s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 470s importlib.import_module(module_name) 470s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 470s return _bootstrap._gcd_import(name[level:], package, level) 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s :1398: in _gcd_import 470s ??? 470s :1371: in _find_and_load 470s ??? 470s :1342: in _find_and_load_unlocked 470s ??? 470s :938: in _load_unlocked 470s ??? 470s :759: in exec_module 470s ??? 470s :491: in _call_with_frames_removed 470s ??? 470s /usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py:30: in 470s from pytest_subtests import SubTests 470s E ModuleNotFoundError: No module named 'pytest_subtests' 470s ERROR src/jobEncapsulationTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py'. 470s Hint: make sure your test modules/packages have valid Python names. 470s Traceback: 470s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 470s mod = import_path( 470s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 470s importlib.import_module(module_name) 470s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 470s return _bootstrap._gcd_import(name[level:], package, level) 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s :1398: in _gcd_import 470s ??? 470s :1371: in _find_and_load 470s ??? 470s :1342: in _find_and_load_unlocked 470s ??? 470s :938: in _load_unlocked 470s ??? 470s :759: in exec_module 470s ??? 470s :491: in _call_with_frames_removed 470s ??? 470s /usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py:17: in 470s from toil.test.src.jobTest import fn1Test 470s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 470s from pytest_subtests import SubTests 470s E ModuleNotFoundError: No module named 'pytest_subtests' 470s ERROR src/jobTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobTest.py'. 470s Hint: make sure your test modules/packages have valid Python names. 470s Traceback: 470s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 470s mod = import_path( 470s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 470s importlib.import_module(module_name) 470s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 470s return _bootstrap._gcd_import(name[level:], package, level) 470s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 470s :1398: in _gcd_import 470s ??? 470s :1371: in _find_and_load 470s ??? 470s :1342: in _find_and_load_unlocked 470s ??? 470s :938: in _load_unlocked 470s ??? 470s :759: in exec_module 470s ??? 470s :491: in _call_with_frames_removed 470s ??? 470s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 470s from pytest_subtests import SubTests 470s E ModuleNotFoundError: No module named 'pytest_subtests' 470s = 15 failed, 224 passed, 136 skipped, 3 errors, 24 subtests passed in 316.55s (0:05:16) = 471s ============================= test session starts ============================== 471s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.13 471s cachedir: .pytest_cache 471s rootdir: /tmp/autopkgtest.IiScC1/autopkgtest_tmp/build 471s configfile: setup.cfg 471s plugins: timeout-2.4.0, typeguard-4.4.4, xdist-3.8.0, cwltest-2.6.20251216093331, pytest_httpserver-1.1.3 471s created: 4/4 workers 471s 4 workers [375 items] 471s 471s scheduling tests via LoadScopeScheduling 471s 471s jobStores/jobStoreTest.py::AWSJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::FileJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s [gw1] [ 0%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::AWSJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s [gw1] [ 0%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::AWSJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_default_gpu_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 471s jobStores/jobStoreTest.py::GoogleJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s [gw2] [ 0%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::GoogleJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s [gw2] [ 1%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::GoogleJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s [gw1] [ 1%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s [gw2] [ 1%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s [gw2] [ 1%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::GoogleJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::AWSJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s [gw1] [ 2%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::AWSJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s [gw2] [ 2%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::GoogleJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s [gw1] [ 2%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::AWSJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s [gw2] [ 2%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s [gw2] [ 3%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s [gw2] [ 3%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::GoogleJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s [gw2] [ 3%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s [gw1] [ 4%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::AWSJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s [gw1] [ 4%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::AWSJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s [gw1] [ 4%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 471s jobStores/jobStoreTest.py::AWSJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw2] [ 4%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw1] [ 5%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw1] [ 5%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw1] [ 5%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw2] [ 5%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw2] [ 6%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw2] [ 6%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw1] [ 6%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::testMultiThreadImportFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw2] [ 6%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw1] [ 7%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testMultiThreadImportFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::testOverlargeJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw2] [ 7%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw2] [ 7%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw1] [ 8%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testOverlargeJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw1] [ 8%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw2] [ 8%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw2] [ 8%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw2] [ 9%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw2] [ 9%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw1] [ 9%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw1] [ 9%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw2] [ 10%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw1] [ 10%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw2] [ 10%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw1] [ 10%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw2] [ 11%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw1] [ 11%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw2] [ 11%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw2] [ 12%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw1] [ 12%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw1] [ 12%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw2] [ 12%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw2] [ 13%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw2] [ 13%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw2] [ 13%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw2] [ 13%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw1] [ 14%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw1] [ 14%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw1] [ 14%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw1] [ 14%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw2] [ 15%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw1] [ 15%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw1] [ 15%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw1] [ 16%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw2] [ 16%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw2] [ 16%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw2] [ 16%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw1] [ 17%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw2] [ 17%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s docs/scriptsTest.py::ToilDocumentationTest::testArguments <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 472s [gw1] [ 17%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw1] [ 17%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw1] [ 18%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw1] [ 18%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw1] [ 18%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw1] [ 18%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s [gw1] [ 19%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 472s lib/dockerTest.py::TestDocker::testDockerClean <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 472s [gw3] [ 19%] PASSED batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_default_gpu_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_get_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw0] [ 19%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::FileJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw3] [ 20%] PASSED batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_get_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_any_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw0] [ 20%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::FileJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [gw3] [ 20%] PASSED batchSystems/test_slurm.py::SlurmTest::test_any_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw0] [ 20%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [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 472s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_mix_sacct_scontrol <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw0] [ 21%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::FileJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [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 472s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw0] [ 21%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [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 472s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw0] [ 22%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s jobStores/jobStoreTest.py::FileJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 472s [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 472s 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 472s [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 472s 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 472s [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 472s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_some_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [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 472s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_argument_list_too_big <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [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 472s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw3] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw3] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw3] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw3] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw3] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw3] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw3] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw3] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw3] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw3] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw3] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw3] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [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 472s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [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 472s batchSystems/test_slurm.py::SlurmTest::test_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw3] [ 27%] PASSED batchSystems/test_slurm.py::SlurmTest::test_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_export <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw3] [ 28%] PASSED batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_export <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw3] [ 28%] PASSED batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_time <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s [gw3] [ 28%] PASSED batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_time <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 472s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 472s [gw0] [ 28%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 473s jobStores/jobStoreTest.py::FileJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 473s [gw0] [ 29%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 474s jobStores/jobStoreTest.py::FileJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 474s [gw3] [ 29%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 474s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 474s [gw2] [ 29%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testArguments <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 477s docs/scriptsTest.py::ToilDocumentationTest::testDocker <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 477s [gw1] [ 29%] FAILED lib/dockerTest.py::TestDocker::testDockerClean <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 477s lib/dockerTest.py::TestDocker::testDockerClean_CRx_FORGO <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 479s [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 480s [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 480s [gw2] [ 30%] FAILED docs/scriptsTest.py::ToilDocumentationTest::testDocker <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 481s docs/scriptsTest.py::ToilDocumentationTest::testDynamic <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 481s [gw1] [ 30%] FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_FORGO <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 482s lib/dockerTest.py::TestDocker::testDockerClean_CRx_STOP <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 484s [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 485s [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 485s [gw1] [ 30%] FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_STOP <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 487s lib/dockerTest.py::TestDocker::testDockerClean_CRx_RM <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 490s [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 490s [gw1] [ 31%] FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_RM <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 490s lib/dockerTest.py::TestDocker::testDockerPipeChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 493s [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 494s [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 494s [gw1] [ 31%] FAILED lib/dockerTest.py::TestDocker::testDockerPipeChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 495s lib/dockerTest.py::TestDocker::testDockerPipeChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 495s [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 495s [gw3] [ 31%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 498s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 498s [gw2] [ 31%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testDynamic <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 498s docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 498s [gw3] [ 32%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 498s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 498s [gw1] [ 32%] FAILED lib/dockerTest.py::TestDocker::testDockerPipeChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 500s lib/dockerTest.py::TestDocker::testNonCachingDockerChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 500s [gw3] [ 32%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 500s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 500s [gw2] [ 32%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 502s docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 502s [gw0] [ 33%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 502s jobStores/jobStoreTest.py::FileJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 502s [gw0] [ 33%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 502s jobStores/jobStoreTest.py::FileJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 502s [gw1] [ 33%] FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 503s lib/dockerTest.py::TestDocker::testNonCachingDockerChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 503s [gw3] [ 33%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 505s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 505s [gw2] [ 34%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 505s docs/scriptsTest.py::ToilDocumentationTest::testHelloworld <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 505s [gw3] [ 34%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 508s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 508s [gw1] [ 34%] FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 508s lib/dockerTest.py::TestDocker::testDockerLogs <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 508s [gw2] [ 34%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testHelloworld <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 511s docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 511s [gw2] [ 35%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 514s docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 514s [gw1] [ 35%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 514s lib/dockerTest.py::TestDocker::testDockerLogs_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 514s [gw2] [ 35%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 517s docs/scriptsTest.py::ToilDocumentationTest::testJobFunctions <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 517s [gw2] [ 36%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testJobFunctions <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 518s docs/scriptsTest.py::ToilDocumentationTest::testManaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 518s [gw1] [ 36%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 520s lib/dockerTest.py::TestDocker::testDockerLogs_Demux <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 520s [gw2] [ 36%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testManaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 522s docs/scriptsTest.py::ToilDocumentationTest::testManaging2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 522s [gw1] [ 36%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 522s lib/dockerTest.py::TestDocker::testDockerLogs_Demux_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 522s [gw2] [ 37%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testManaging2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 525s docs/scriptsTest.py::ToilDocumentationTest::testPromises <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 525s [gw2] [ 37%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testPromises <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 527s docs/scriptsTest.py::ToilDocumentationTest::testPromises2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 527s [gw1] [ 37%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 527s src/dockerCheckTest.py::DockerCheckTest::testApplianceParser <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 527s [gw1] [ 37%] PASSED src/dockerCheckTest.py::DockerCheckTest::testApplianceParser <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 527s src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 527s [gw1] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s [gw1] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s [gw1] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s [gw1] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s [gw1] [ 39%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s [gw1] [ 39%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s [gw1] [ 39%] PASSED src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s [gw1] [ 40%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s [gw1] [ 40%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s src/dockerCheckTest.py::DockerCheckTest::testToilQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s [gw1] [ 40%] PASSED src/dockerCheckTest.py::DockerCheckTest::testToilQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 528s provisioners/clusterScalerTest.py::ClusterScalerTest::testBetaInertia <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 528s [gw1] [ 40%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testBetaInertia <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 528s provisioners/clusterScalerTest.py::ClusterScalerTest::testMaxNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 528s [gw1] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testMaxNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 528s provisioners/clusterScalerTest.py::ClusterScalerTest::testMinNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 528s [gw1] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testMinNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 528s provisioners/clusterScalerTest.py::ClusterScalerTest::testNoLaunchingIfDeltaAlreadyMet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s [gw1] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testNoLaunchingIfDeltaAlreadyMet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitIsSet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s [gw1] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitIsSet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitResponse <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s [gw1] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitResponse <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s provisioners/clusterScalerTest.py::ClusterScalerTest::testRounding <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s [gw1] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testRounding <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_large <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s [gw1] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_large <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_observed <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s [gw1] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_observed <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_small <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s [gw1] [ 43%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_small <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s server/serverTest.py::ToilWESServerWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 43%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 43%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 47%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 47%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 47%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s [gw1] [ 51%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 529s provisioners/clusterScalerTest.py::BinPackingTest::testAddingInitialNode <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s [gw1] [ 51%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testAddingInitialNode <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s provisioners/clusterScalerTest.py::BinPackingTest::testHighTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s [gw1] [ 51%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testHighTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s provisioners/clusterScalerTest.py::BinPackingTest::testJobTooLargeForAllNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s [gw1] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testJobTooLargeForAllNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s provisioners/clusterScalerTest.py::BinPackingTest::testLongRunningJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s [gw1] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testLongRunningJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s provisioners/clusterScalerTest.py::BinPackingTest::testLowTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s [gw1] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testLowTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s provisioners/clusterScalerTest.py::BinPackingTest::testPackingOneShape <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s [gw1] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testPackingOneShape <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s provisioners/clusterScalerTest.py::BinPackingTest::testPathologicalCase <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s [gw1] [ 53%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testPathologicalCase <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s provisioners/clusterScalerTest.py::BinPackingTest::testSorting <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s [gw1] [ 53%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testSorting <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s provisioners/clusterScalerTest.py::BinPackingTest::testZeroResourceJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s [gw1] [ 53%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testZeroResourceJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 529s utils/utilsTest.py::TestUtils::test_config_functionality <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 529s [gw1] [ 53%] PASSED utils/utilsTest.py::TestUtils::test_config_functionality <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 542s utils/utilsTest.py::TestUtils::testUtilsSort <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 542s [gw2] [ 54%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testPromises2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 545s docs/scriptsTest.py::ToilDocumentationTest::testQuickstart <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 545s [gw2] [ 54%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testQuickstart <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 553s docs/scriptsTest.py::ToilDocumentationTest::testRequirements <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 553s [gw2] [ 54%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testRequirements <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 556s docs/scriptsTest.py::ToilDocumentationTest::testStaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 556s [gw2] [ 54%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testStaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 560s docs/scriptsTest.py::ToilDocumentationTest::testStats <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 560s [gw0] [ 55%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s [gw0] [ 55%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s [gw0] [ 55%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s [gw0] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s [gw0] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s [gw0] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s [gw0] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s [gw0] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s [gw0] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s [gw0] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s [gw0] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s [gw0] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s [gw0] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::test_file_link_imports <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s [gw0] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_file_link_imports <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_does_not_leak_symlinks <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s [gw0] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_does_not_leak_symlinks <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_init_preserves_symlink_path <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s [gw0] [ 59%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_init_preserves_symlink_path <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::test_symlink_read_control <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s [gw0] [ 59%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_symlink_read_control <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s [gw0] [ 59%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s [gw0] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s [gw0] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s [gw0] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s [gw0] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s [gw0] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s [gw0] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s [gw0] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s [gw0] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 560s [gw0] [ 62%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 561s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 561s [gw0] [ 62%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 561s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 561s [gw0] [ 62%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 561s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 561s [gw0] [ 62%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 561s lib/test_url.py::TestURLAccess::test_get_url_access <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 561s [gw0] [ 63%] PASSED lib/test_url.py::TestURLAccess::test_get_url_access <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 561s lib/test_url.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 561s [gw0] [ 63%] SKIPPED lib/test_url.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 561s lib/test_url.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 561s [gw0] [ 63%] SKIPPED lib/test_url.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 561s lib/test_url.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 561s [gw0] [ 64%] SKIPPED lib/test_url.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 561s lib/test_url.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 561s [gw0] [ 64%] SKIPPED lib/test_url.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 561s lib/test_url.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 561s [gw0] [ 64%] SKIPPED lib/test_url.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 561s lib/url_plugin_test.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 561s [gw0] [ 64%] PASSED lib/url_plugin_test.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 561s lib/url_plugin_test.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 561s [gw0] [ 65%] PASSED lib/url_plugin_test.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 561s lib/url_plugin_test.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 561s [gw0] [ 65%] PASSED lib/url_plugin_test.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 561s lib/url_plugin_test.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 561s [gw0] [ 65%] PASSED lib/url_plugin_test.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 561s lib/url_plugin_test.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 561s [gw0] [ 65%] PASSED lib/url_plugin_test.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 561s lib/url_plugin_test.py::TestURLAccess::test_url_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 561s [gw0] [ 66%] PASSED lib/url_plugin_test.py::TestURLAccess::test_url_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 563s src/retainTempDirTest.py::TestCleanWorkDir::testNever <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 563s [gw0] [ 66%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testNever <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 566s src/retainTempDirTest.py::TestCleanWorkDir::testAlways <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 566s [gw0] [ 66%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testAlways <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 571s src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 571s [gw0] [ 66%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 573s src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithNoError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 573s [gw0] [ 67%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithNoError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 578s src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 578s [gw1] [ 67%] PASSED utils/utilsTest.py::TestUtils::testUtilsSort <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 578s utils/utilsTest.py::TestUtils::testUnicodeSupport <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 578s [gw0] [ 67%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 580s src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithSuccess <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 580s [gw2] [ 68%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testStats <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 580s src/miscTests.py::TestMisc::testIDStability <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 580s [gw2] [ 68%] PASSED src/miscTests.py::TestMisc::testIDStability <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 580s src/miscTests.py::TestMisc::test_atomic_install <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 580s [gw2] [ 68%] PASSED src/miscTests.py::TestMisc::test_atomic_install <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 580s src/miscTests.py::TestMisc::test_atomic_install_dev <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 580s [gw2] [ 68%] PASSED src/miscTests.py::TestMisc::test_atomic_install_dev <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 580s src/miscTests.py::TestMisc::test_atomic_context_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 580s [gw2] [ 69%] PASSED src/miscTests.py::TestMisc::test_atomic_context_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 580s src/miscTests.py::TestMisc::test_atomic_context_error <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 580s [gw2] [ 69%] PASSED src/miscTests.py::TestMisc::test_atomic_context_error <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 580s src/miscTests.py::TestMisc::test_call_command_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 580s [gw2] [ 69%] PASSED src/miscTests.py::TestMisc::test_call_command_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 580s src/miscTests.py::TestMisc::test_call_command_err <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 580s [gw2] [ 69%] PASSED src/miscTests.py::TestMisc::test_call_command_err <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 580s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s [gw1] [ 70%] PASSED utils/utilsTest.py::TestUtils::testUnicodeSupport <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 580s utils/utilsTest.py::TestUtils::testGetPIDStatus <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 580s [gw0] [ 70%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithSuccess <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 580s lib/aws/test_utils.py::TagGenerationTest::test_build_tag <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 580s [gw0] [ 70%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_build_tag <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 580s lib/aws/test_utils.py::TagGenerationTest::test_build_tag_with_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 580s [gw0] [ 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 580s lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 580s [gw0] [ 71%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 580s lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 580s [gw0] [ 71%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 580s lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 580s [gw0] [ 71%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 580s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s [gw0] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s [gw0] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s [gw0] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s [gw0] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s [gw0] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s [gw0] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s [gw0] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s [gw0] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s [gw0] [ 74%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s [gw0] [ 74%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 580s src/resourceTest.py::TestResource::testStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 580s [gw0] [ 74%] PASSED src/resourceTest.py::TestResource::testStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 580s src/resourceTest.py::TestResource::testPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 580s [gw0] [ 74%] PASSED src/resourceTest.py::TestResource::testPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 580s src/resourceTest.py::TestResource::testStandAloneInPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 580s [gw0] [ 75%] PASSED src/resourceTest.py::TestResource::testStandAloneInPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 581s src/resourceTest.py::TestResource::testBuiltIn <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 581s [gw0] [ 75%] PASSED src/resourceTest.py::TestResource::testBuiltIn <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 581s src/resourceTest.py::TestResource::testNonPyStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 581s [gw0] [ 75%] PASSED src/resourceTest.py::TestResource::testNonPyStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 583s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 583s [gw0] [ 76%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 583s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithClassMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 585s [gw2] [ 76%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 585s [gw1] [ 76%] PASSED utils/utilsTest.py::TestUtils::testGetPIDStatus <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 586s utils/utilsTest.py::TestUtils::testGetStatusFailedToilWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 586s [gw0] [ 76%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithClassMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 586s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithLambda <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 588s [gw2] [ 76%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 588s [gw0] [ 77%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithLambda <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 589s src/deferredFunctionTest.py::TestDeferredFunction::testBatchSystemCleanupCanHandleWorkerDeaths <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 590s [gw2] [ 77%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 590s [gw1] [ 77%] PASSED utils/utilsTest.py::TestUtils::testGetStatusFailedToilWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 591s utils/utilsTest.py::TestUtils::testGetStatusFailedCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 593s [gw2] [ 77%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 593s [gw0] [ 77%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testBatchSystemCleanupCanHandleWorkerDeaths <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 593s src/miscTests.py::TestPanic::test_panic_by_hand <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 593s [gw0] [ 77%] PASSED src/miscTests.py::TestPanic::test_panic_by_hand <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 593s src/miscTests.py::TestPanic::test_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 593s [gw0] [ 78%] PASSED src/miscTests.py::TestPanic::test_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 593s src/miscTests.py::TestPanic::test_panic_with_secondary <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 593s [gw0] [ 78%] PASSED src/miscTests.py::TestPanic::test_panic_with_secondary <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 593s src/miscTests.py::TestPanic::test_nested_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 593s [gw0] [ 78%] PASSED src/miscTests.py::TestPanic::test_nested_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 593s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 593s [gw0] [ 78%] 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 593s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 593s [gw0] [ 79%] PASSED batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 593s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_still_running <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 593s [gw0] [ 79%] 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 593s lib/test_conversions.py::ConversionTest::test_convert <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 593s [gw0] [ 79%] PASSED lib/test_conversions.py::ConversionTest::test_convert <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 593s lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 593s [gw0] [ 80%] PASSED lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 593s lib/test_conversions.py::ConversionTest::test_human2bytes <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 593s [gw0] [ 80%] PASSED lib/test_conversions.py::ConversionTest::test_human2bytes <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 593s lib/test_history.py::TestHistory::test_history_submittable_detection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 593s [gw0] [ 80%] PASSED lib/test_history.py::TestHistory::test_history_submittable_detection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 593s lib/test_history.py::TestHistory::test_history_deletion <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 593s [gw0] [ 80%] PASSED lib/test_history.py::TestHistory::test_history_deletion <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 593s lib/test_history.py::TestHistory::test_history_size_limit <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 593s [gw0] [ 81%] PASSED lib/test_history.py::TestHistory::test_history_size_limit <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 593s server/serverTest.py::ToilWESServerBenchTest::test_get_service_info <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 593s [gw0] [ 81%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_get_service_info <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 593s server/serverTest.py::ToilWESServerBenchTest::test_health <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 593s [gw0] [ 81%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_health <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 593s server/serverTest.py::ToilWESServerBenchTest::test_home <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 593s [gw0] [ 81%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_home <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 593s src/busTest.py::TestMessageBus::test_enum_ints_in_file <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 593s [gw0] [ 82%] PASSED src/busTest.py::TestMessageBus::test_enum_ints_in_file <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 593s src/busTest.py::TestMessageBus::test_cross_thread_messaging <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 593s [gw0] [ 82%] PASSED src/busTest.py::TestMessageBus::test_cross_thread_messaging <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 594s src/busTest.py::TestMessageBus::test_restart_without_bus_path <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 596s [gw2] [ 82%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 596s [gw1] [ 82%] PASSED utils/utilsTest.py::TestUtils::testGetStatusFailedCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 596s utils/utilsTest.py::TestUtils::testGetStatusSuccessfulCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 599s [gw2] [ 82%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 600s [gw2] [ 82%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 600s [gw1] [ 82%] PASSED utils/utilsTest.py::TestUtils::testGetStatusSuccessfulCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 601s utils/utilsTest.py::TestUtils::testPrintJobLog <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 601s [gw2] [ 82%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 601s [gw2] [ 82%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 602s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 602s [gw0] [ 83%] PASSED src/busTest.py::TestMessageBus::test_restart_without_bus_path <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 604s src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 604s [gw2] [ 83%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 605s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 605s [gw1] [ 83%] PASSED utils/utilsTest.py::TestUtils::testPrintJobLog <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 605s utils/utilsTest.py::TestUtils::testRestartAttribute <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 605s [gw0] [ 84%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 611s src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 611s [gw2] [ 84%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 612s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 612s [gw0] [ 84%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 614s src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 614s [gw0] [ 84%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 614s src/promisedRequirementTest.py::TestMesosPromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 614s [gw0] [ 85%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 614s src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 614s [gw0] [ 85%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 614s src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 614s [gw0] [ 85%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 616s utils/toilDebugTest.py::TestDebugJob::test_run_job <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 616s [gw2] [ 85%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 619s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 619s [gw2] [ 86%] SUBPASSED[Testing readwrite file permissions 619s [executable: True] 619s [caching: True] 620s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 620s [gw0] [ 86%] PASSED utils/toilDebugTest.py::TestDebugJob::test_run_job <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 621s utils/toilDebugTest.py::TestDebugJob::test_print_job_info <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 621s [gw2] [ 86%] SUBPASSED[Testing readwrite file permissions 621s [executable: True] 621s [caching: False] 624s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 624s [gw2] [ 86%] SUBPASSED[Testing readwrite file permissions 624s [executable: False] 624s [caching: True] 624s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 624s [gw1] [ 86%] PASSED utils/utilsTest.py::TestUtils::testRestartAttribute <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 626s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 626s [gw0] [ 86%] PASSED utils/toilDebugTest.py::TestDebugJob::test_print_job_info <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 626s utils/toilDebugTest.py::TestDebugJob::test_retrieve_task_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 626s [gw0] [ 87%] SKIPPED utils/toilDebugTest.py::TestDebugJob::test_retrieve_task_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 626s __init__.py::toil.test.make_tests <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 626s [gw0] [ 87%] PASSED __init__.py::toil.test.make_tests <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 627s __init__.py::toil.test.timeLimit <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 627s [gw2] [ 87%] SUBPASSED[Testing readwrite file permissions 627s [executable: False] 627s [caching: False] 627s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 627s [gw2] [ 87%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 627s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 627s [gw2] [ 87%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 628s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 628s [gw0] [ 88%] PASSED __init__.py::toil.test.timeLimit <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 628s options/options.py::OptionsTest::test_caching_option_priority <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 628s [gw0] [ 88%] PASSED options/options.py::OptionsTest::test_caching_option_priority <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 628s options/options.py::OptionsTest::test_default_caching_slurm <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 628s [gw0] [ 88%] PASSED options/options.py::OptionsTest::test_default_caching_slurm <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 628s src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 628s [gw0] [ 88%] PASSED src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 628s src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 628s [gw0] [ 89%] PASSED src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 631s src/threadingTest.py::TestThreading::testGlobalMutexOrdering <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 631s [gw2] [ 89%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 631s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 631s [gw2] [ 89%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 631s server/serverTest.py::AWSStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 631s [gw2] [ 89%] SKIPPED server/serverTest.py::AWSStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 631s server/serverTest.py::AWSStateStoreTest::test_state_store_paths <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 631s [gw2] [ 90%] SKIPPED server/serverTest.py::AWSStateStoreTest::test_state_store_paths <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 631s 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 631s [gw2] [ 90%] 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 631s jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 631s [gw2] [ 90%] SKIPPED jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 631s lib/test_misc.py::UserNameAvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 631s [gw2] [ 90%] PASSED lib/test_misc.py::UserNameAvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 631s lib/test_misc.py::UserNameUnvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 631s [gw2] [ 91%] PASSED lib/test_misc.py::UserNameUnvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 631s lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 631s [gw2] [ 91%] PASSED lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 631s mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue <- ../../../../usr/lib/python3/dist-packages/toil/test/mesos/MesosDataStructuresTest.py 631s [gw2] [ 91%] PASSED mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue <- ../../../../usr/lib/python3/dist-packages/toil/test/mesos/MesosDataStructuresTest.py 631s provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/provisionerTest.py 631s [gw2] [ 92%] PASSED provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/provisionerTest.py 631s server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 631s [gw2] [ 92%] SKIPPED server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 631s server/serverTest.py::FileStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 631s [gw2] [ 92%] SKIPPED server/serverTest.py::FileStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 631s server/serverTest.py::FileStateStoreURLTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 631s [gw2] [ 92%] SKIPPED server/serverTest.py::FileStateStoreURLTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 632s src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried <- ../../../../usr/lib/python3/dist-packages/toil/test/src/checkpointTest.py 632s [gw1] [ 93%] PASSED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 633s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 633s [gw0] [ 93%] PASSED src/threadingTest.py::TestThreading::testGlobalMutexOrdering <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 636s src/threadingTest.py::TestThreading::testLastProcessStanding <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 636s [gw0] [ 93%] PASSED src/threadingTest.py::TestThreading::testLastProcessStanding <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 636s batchSystems/batch_system_plugin_test.py::BatchSystemPluginTest::test_batchsystem_plugin_installable <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batch_system_plugin_test.py 636s [gw0] [ 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 637s src/jobServiceTest.py::TestPerfectServicet::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 637s [gw2] [ 94%] PASSED src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried <- ../../../../usr/lib/python3/dist-packages/toil/test/src/checkpointTest.py 639s src/environmentTest.py::EnvironmentTest::test_environment <- ../../../../usr/lib/python3/dist-packages/toil/test/src/environmentTest.py 639s [gw1] [ 94%] PASSED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 646s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 646s [gw1] [ 94%] PASSED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 651s src/jobServiceTest.py::TestJobService::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 651s [gw2] [ 94%] PASSED src/environmentTest.py::EnvironmentTest::test_environment <- ../../../../usr/lib/python3/dist-packages/toil/test/src/environmentTest.py 657s src/helloWorldTest.py::HelloWorldTest::testHelloWorld <- ../../../../usr/lib/python3/dist-packages/toil/test/src/helloWorldTest.py 657s [gw2] [ 95%] PASSED src/helloWorldTest.py::HelloWorldTest::testHelloWorld <- ../../../../usr/lib/python3/dist-packages/toil/test/src/helloWorldTest.py 658s src/promisesTest.py::PathIndexingPromiseTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 658s [gw0] [ 95%] PASSED src/jobServiceTest.py::TestPerfectServicet::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 659s src/promisesTest.py::CachedUnpicklingJobStoreTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 659s [gw2] [ 95%] PASSED src/promisesTest.py::PathIndexingPromiseTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 661s src/systemTest.py::TestSystem::testAtomicityOfNonEmptyDirectoryRenames <- ../../../../usr/lib/python3/dist-packages/toil/test/src/systemTest.py 661s [gw2] [ 96%] PASSED src/systemTest.py::TestSystem::testAtomicityOfNonEmptyDirectoryRenames <- ../../../../usr/lib/python3/dist-packages/toil/test/src/systemTest.py 661s src/workerTest.py::WorkerTests::testNextChainable <- ../../../../usr/lib/python3/dist-packages/toil/test/src/workerTest.py 661s [gw2] [ 96%] PASSED src/workerTest.py::WorkerTests::testNextChainable <- ../../../../usr/lib/python3/dist-packages/toil/test/src/workerTest.py 661s utils/toilKillTest.py::TestToilKill::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 661s [gw2] [ 96%] SKIPPED utils/toilKillTest.py::TestToilKill::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 661s utils/toilKillTest.py::TestToilKillWithAWSJobStore::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 663s [gw2] [ 96%] SKIPPED utils/toilKillTest.py::TestToilKillWithAWSJobStore::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 663s [gw0] [ 97%] PASSED src/promisesTest.py::CachedUnpicklingJobStoreTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 666s src/promisesTest.py::ChainedIndexedPromisesTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 666s [gw0] [ 97%] PASSED src/promisesTest.py::ChainedIndexedPromisesTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 672s utils/toilDebugTest.py::testFetchJobStoreFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 677s [gw0] [ 97%] PASSED utils/toilDebugTest.py::testFetchJobStoreFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 677s [gw1] [ 97%] PASSED src/jobServiceTest.py::TestJobService::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 679s src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger <- ../../../../usr/lib/python3/dist-packages/toil/test/src/realtimeLoggerTest.py 679s [gw1] [ 98%] PASSED src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger <- ../../../../usr/lib/python3/dist-packages/toil/test/src/realtimeLoggerTest.py 686s src/resumabilityTest.py::TestResumability::test_chaining <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resumabilityTest.py 754s [gw1] [ 98%] PASSED src/resumabilityTest.py::TestResumability::test_chaining <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resumabilityTest.py 754s [gw3] [ 98%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 761s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 761s [gw3] [ 98%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 766s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 766s [gw3] [ 99%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 768s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 768s [gw3] [ 99%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 771s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 771s [gw3] [ 99%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 773s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 773s [gw3] [100%] SUBPASSED[Testing readwrite file permissions 773s [executable: True] 773s [caching: True] 776s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 776s [gw3] [100%] SUBPASSED[Testing readwrite file permissions 776s [executable: True] 776s [caching: False] 778s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 778s [gw3] [100%] SUBPASSED[Testing readwrite file permissions 778s [executable: False] 778s [caching: True] 781s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 781s [gw3] [100%] SUBPASSED[Testing readwrite file permissions 781s [executable: False] 781s [caching: False] 781s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 781s [gw3] [100%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 781s 781s ==================================== ERRORS ==================================== 781s _________________ ERROR collecting src/importExportFileTest.py _________________ 781s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py'. 781s Hint: make sure your test modules/packages have valid Python names. 781s Traceback: 781s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 781s mod = import_path( 781s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 781s importlib.import_module(module_name) 781s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 781s return _bootstrap._gcd_import(name[level:], package, level) 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s :1387: in _gcd_import 781s ??? 781s :1360: in _find_and_load 781s ??? 781s :1331: in _find_and_load_unlocked 781s ??? 781s :935: in _load_unlocked 781s ??? 781s :1023: in exec_module 781s ??? 781s :488: in _call_with_frames_removed 781s ??? 781s /usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py:30: in 781s from pytest_subtests import SubTests 781s E ModuleNotFoundError: No module named 'pytest_subtests' 781s _________________ ERROR collecting src/jobEncapsulationTest.py _________________ 781s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py'. 781s Hint: make sure your test modules/packages have valid Python names. 781s Traceback: 781s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 781s mod = import_path( 781s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 781s importlib.import_module(module_name) 781s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 781s return _bootstrap._gcd_import(name[level:], package, level) 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s :1387: in _gcd_import 781s ??? 781s :1360: in _find_and_load 781s ??? 781s :1331: in _find_and_load_unlocked 781s ??? 781s :935: in _load_unlocked 781s ??? 781s :1023: in exec_module 781s ??? 781s :488: in _call_with_frames_removed 781s ??? 781s /usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py:17: in 781s from toil.test.src.jobTest import fn1Test 781s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 781s from pytest_subtests import SubTests 781s E ModuleNotFoundError: No module named 'pytest_subtests' 781s _______________________ ERROR collecting src/jobTest.py ________________________ 781s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobTest.py'. 781s Hint: make sure your test modules/packages have valid Python names. 781s Traceback: 781s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 781s mod = import_path( 781s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 781s importlib.import_module(module_name) 781s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 781s return _bootstrap._gcd_import(name[level:], package, level) 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s :1387: in _gcd_import 781s ??? 781s :1360: in _find_and_load 781s ??? 781s :1331: in _find_and_load_unlocked 781s ??? 781s :935: in _load_unlocked 781s ??? 781s :1023: in exec_module 781s ??? 781s :488: in _call_with_frames_removed 781s ??? 781s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 781s from pytest_subtests import SubTests 781s E ModuleNotFoundError: No module named 'pytest_subtests' 781s =================================== FAILURES =================================== 781s __________________________ TestDocker.testDockerClean __________________________ 781s [gw1] linux -- Python 3.13.11 /usr/bin/python3.13 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 781s toil.start(A) 781s ~~~~~~~~~~^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 781s return self._runMainLoop(rootJobDescription) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 781s ).run() 781s ~~~^^ 781s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 781s raise FailedJobsException( 781s ...<3 lines>... 781s ) 781s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v3 781s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v3" follows: 781s =========> 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v1 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v1 781s [2026-01-30T23:47:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju 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. 781s [2026-01-30T23:47:49+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 781s apiDockerCall( 781s ~~~~~~~~~~~~~^ 781s job, 781s ^^^^ 781s ...<6 lines>... 781s privileged=True, 781s ^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:47:49+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 781s result: TResult | None = func() 781s ~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 781s lambda: runtest_hook(item=item, **kwds), 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 781s yield 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 781s return result.get_result() 781s ~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 781s raise exc.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 781s res = yield 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 781s item.runtest() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 781s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 781s result = testfunction(**testargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 781s file_stats = test_file.stat() 781s File "/usr/lib/python3.13/pathlib/_local.py", line 517, in stat 781s return os.stat(self, follow_symlinks=follow_symlinks) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean0/working/test.txt' 781s ----------------------------- Captured stderr call ----------------------------- 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of ec33b958-d93d-4e15-919f-46806d490b9a in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean0/jobstore 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil.lib.history] Workflow ec33b958-d93d-4e15-919f-46806d490b9a is a run of 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:47:49+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-gw1/testDockerClean0/jobstore kind-_testDockerCleanFn/instance-k1x9wuju. 781s [2026-01-30T23:47:49+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v1 781s Exit reason: None 781s [2026-01-30T23:47:49+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v2 781s [2026-01-30T23:47:49+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-k1x9wuju" follows: 781s =========> 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v1 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v1 781s [2026-01-30T23:47:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju 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. 781s [2026-01-30T23:47:49+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 781s apiDockerCall( 781s ~~~~~~~~~~~~~^ 781s job, 781s ^^^^ 781s ...<6 lines>... 781s privileged=True, 781s ^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:47:49+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:47:49+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v2 with ID kind-_testDockerCleanFn/instance-k1x9wuju to 0 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 781s [2026-01-30T23:47:49+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v3 is completely failed 781s [2026-01-30T23:47:49+0000] [Thread-5 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:47:49: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju 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. 781s [2026-01-30T23:47:53+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s [2026-01-30T23:47:53+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 781s [2026-01-30T23:47:53+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v3 781s [2026-01-30T23:47:53+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil.lib.history] Workflow ec33b958-d93d-4e15-919f-46806d490b9a stopped. Success: False 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean0/jobstore) 781s ------------------------------ Captured log call ------------------------------- 781s INFO  toil.lib.history:history.py:369 Recording workflow creation of ec33b958-d93d-4e15-919f-46806d490b9a in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean0/jobstore 781s INFO  toil.lib.history:history.py:399 Workflow ec33b958-d93d-4e15-919f-46806d490b9a is a run of 781s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s 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-gw1/testDockerClean0/jobstore kind-_testDockerCleanFn/instance-k1x9wuju. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v1 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v2 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-k1x9wuju" follows: 781s =========> 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v1 781s [2026-01-30T23:47:49+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v1 781s [2026-01-30T23:47:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju 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. 781s [2026-01-30T23:47:49+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 781s apiDockerCall( 781s ~~~~~~~~~~~~~^ 781s job, 781s ^^^^ 781s ...<6 lines>... 781s privileged=True, 781s ^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:47:49+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v2 with ID kind-_testDockerCleanFn/instance-k1x9wuju to 0 781s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 781s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v3 is completely failed 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:47:49: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju 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. 781s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 781s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k1x9wuju v3 781s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 781s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 781s INFO  toil.lib.history:history.py:530 Workflow ec33b958-d93d-4e15-919f-46806d490b9a stopped. Success: False 781s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean0/jobstore) 781s _______________________ ToilDocumentationTest.testDocker _______________________ 781s [gw2] linux -- Python 3.13.11 /usr/bin/python3.13 781s Traceback (most recent call last): 781s File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor 781s yield 781s File "/usr/lib/python3.13/unittest/case.py", line 651, in run 781s self._callTestMethod(testMethod) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod 781s if method() is not None: 781s ~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py", line 161, in testDocker 781s self.checkExitCode("tutorial_docker.py") 781s ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py", line 50, in checkExitCode 781s raise RuntimeError(stderr) 781s RuntimeError: [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of adbfe9cd-77b8-4e6c-bcca-28b3dd2ed937 in file:/tmp/tmpsmktma36tutorial_docker 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.lib.history] Workflow adbfe9cd-77b8-4e6c-bcca-28b3dd2ed937 is a run of /usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:47:52+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmpsmktma36tutorial_docker kind-apiDockerCall/instance-tdpmx00b. 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v1 781s Exit reason: None 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v2 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-tdpmx00b" follows: 781s =========> 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v1 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v1) from description 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v1 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b 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. 781s [2026-01-30T23:47:52+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:47:52+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v2 with ID kind-apiDockerCall/instance-tdpmx00b to 1 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:47:52+0000] [Thread-4 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:47:52: Job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b 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. 781s [2026-01-30T23:47:52+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmpsmktma36tutorial_docker kind-apiDockerCall/instance-tdpmx00b. 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v3 781s Exit reason: None 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v5 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-tdpmx00b" follows: 781s =========> 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v4 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v4) from description 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v4 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b 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. 781s [2026-01-30T23:47:52+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:47:52+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v5 with ID kind-apiDockerCall/instance-tdpmx00b to 0 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.leader] Job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v6 is completely failed 781s [2026-01-30T23:47:53+0000] [Thread-4 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:47:53: Job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b 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. 781s [2026-01-30T23:47:56+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s [2026-01-30T23:47:56+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 781s [2026-01-30T23:47:56+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v6 781s [2026-01-30T23:47:56+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 781s [2026-01-30T23:47:56+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 781s [2026-01-30T23:47:56+0000] [MainThread] [I] [toil.lib.history] Workflow adbfe9cd-77b8-4e6c-bcca-28b3dd2ed937 stopped. Success: False 781s [2026-01-30T23:47:56+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/tmpsmktma36tutorial_docker) 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py", line 20, in 781s toil.start(align) 781s ~~~~~~~~~~^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 781s return self._runMainLoop(rootJobDescription) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 781s ).run() 781s ~~~^^ 781s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 781s raise FailedJobsException( 781s ...<3 lines>... 781s ) 781s toil.exceptions.FailedJobsException: The job store '/tmp/tmpsmktma36tutorial_docker' contains 1 failed jobs: 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v6 781s Log from job "'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v6" follows: 781s =========> 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v4 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v4) from description 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v4 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b 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. 781s [2026-01-30T23:47:52+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:47:52+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s 781s ---------------------------- Captured stdout setup ----------------------------- 781s 781s 781s [TEST] toil.test.docs.scriptsTest.ToilDocumentationTest:testDocker (Jan 30 2026 15:47:51:881296 PST) 781s 781s 781s _____________________ TestDocker.testDockerClean_CRx_FORGO _____________________ 781s [gw1] linux -- Python 3.13.11 /usr/bin/python3.13 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 781s toil.start(A) 781s ~~~~~~~~~~^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 781s return self._runMainLoop(rootJobDescription) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 781s ).run() 781s ~~~^^ 781s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 781s raise FailedJobsException( 781s ...<3 lines>... 781s ) 781s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_FORGO0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v3 781s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v3" follows: 781s =========> 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v1 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v1 781s [2026-01-30T23:47:54+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 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. 781s [2026-01-30T23:47:54+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 781s apiDockerCall( 781s ~~~~~~~~~~~~~^ 781s job, 781s ^^^^ 781s ...<6 lines>... 781s privileged=True, 781s ^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:47:54+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 781s result: TResult | None = func() 781s ~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 781s lambda: runtest_hook(item=item, **kwds), 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 781s yield 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 781s return result.get_result() 781s ~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 781s raise exc.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 781s res = yield 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 781s item.runtest() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 781s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 781s result = testfunction(**testargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 133, in testDockerClean_CRx_FORGO 781s self.testDockerClean( 781s ~~~~~~~~~~~~~~~~~~~~^ 781s tmp_path, caching=False, detached=False, rm=True, deferParam=FORGO 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 781s file_stats = test_file.stat() 781s File "/usr/lib/python3.13/pathlib/_local.py", line 517, in stat 781s return os.stat(self, follow_symlinks=follow_symlinks) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_FORGO0/working/test.txt' 781s ----------------------------- Captured stderr call ----------------------------- 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 2a71261c-98bd-4ca3-9f8f-add6c1175042 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_FORGO0/jobstore 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil.lib.history] Workflow 2a71261c-98bd-4ca3-9f8f-add6c1175042 is a run of 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:47:54+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-gw1/testDockerClean_CRx_FORGO0/jobstore kind-_testDockerCleanFn/instance-5jlwuqm5. 781s [2026-01-30T23:47:54+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v1 781s Exit reason: None 781s [2026-01-30T23:47:54+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v2 781s [2026-01-30T23:47:54+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-5jlwuqm5" follows: 781s =========> 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v1 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v1 781s [2026-01-30T23:47:54+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 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. 781s [2026-01-30T23:47:54+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 781s apiDockerCall( 781s ~~~~~~~~~~~~~^ 781s job, 781s ^^^^ 781s ...<6 lines>... 781s privileged=True, 781s ^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:47:54+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:47:54+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v2 with ID kind-_testDockerCleanFn/instance-5jlwuqm5 to 0 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 781s [2026-01-30T23:47:54+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v3 is completely failed 781s [2026-01-30T23:47:54+0000] [Thread-9 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:47:54: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 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. 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v3 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.lib.history] Workflow 2a71261c-98bd-4ca3-9f8f-add6c1175042 stopped. Success: False 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_FORGO0/jobstore) 781s ------------------------------ Captured log call ------------------------------- 781s INFO  toil.lib.history:history.py:369 Recording workflow creation of 2a71261c-98bd-4ca3-9f8f-add6c1175042 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_FORGO0/jobstore 781s INFO  toil.lib.history:history.py:399 Workflow 2a71261c-98bd-4ca3-9f8f-add6c1175042 is a run of 781s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s 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-gw1/testDockerClean_CRx_FORGO0/jobstore kind-_testDockerCleanFn/instance-5jlwuqm5. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v1 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v2 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-5jlwuqm5" follows: 781s =========> 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v1 781s [2026-01-30T23:47:54+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v1 781s [2026-01-30T23:47:54+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 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. 781s [2026-01-30T23:47:54+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 781s apiDockerCall( 781s ~~~~~~~~~~~~~^ 781s job, 781s ^^^^ 781s ...<6 lines>... 781s privileged=True, 781s ^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:47:54+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v2 with ID kind-_testDockerCleanFn/instance-5jlwuqm5 to 0 781s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 781s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v3 is completely failed 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:47:54: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 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. 781s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 781s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-5jlwuqm5 v3 781s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 781s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 781s INFO  toil.lib.history:history.py:530 Workflow 2a71261c-98bd-4ca3-9f8f-add6c1175042 stopped. Success: False 781s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_FORGO0/jobstore) 781s _____________________ TestDocker.testDockerClean_CRx_STOP ______________________ 781s [gw1] linux -- Python 3.13.11 /usr/bin/python3.13 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 781s toil.start(A) 781s ~~~~~~~~~~^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 781s return self._runMainLoop(rootJobDescription) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 781s ).run() 781s ~~~^^ 781s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 781s raise FailedJobsException( 781s ...<3 lines>... 781s ) 781s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_STOP0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v3 781s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v3" follows: 781s =========> 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v1 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v1 781s [2026-01-30T23:47:58+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 781s apiDockerCall( 781s ~~~~~~~~~~~~~^ 781s job, 781s ^^^^ 781s ...<6 lines>... 781s privileged=True, 781s ^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:47:58+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 781s result: TResult | None = func() 781s ~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 781s lambda: runtest_hook(item=item, **kwds), 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 781s yield 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 781s return result.get_result() 781s ~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 781s raise exc.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 781s res = yield 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 781s item.runtest() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 781s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 781s result = testfunction(**testargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 138, in testDockerClean_CRx_STOP 781s self.testDockerClean( 781s ~~~~~~~~~~~~~~~~~~~~^ 781s tmp_path, caching=False, detached=False, rm=True, deferParam=STOP 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 781s file_stats = test_file.stat() 781s File "/usr/lib/python3.13/pathlib/_local.py", line 517, in stat 781s return os.stat(self, follow_symlinks=follow_symlinks) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_STOP0/working/test.txt' 781s ----------------------------- Captured stderr call ----------------------------- 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of d2f03a72-8f01-4fce-bcfa-421482d305b6 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_STOP0/jobstore 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.lib.history] Workflow d2f03a72-8f01-4fce-bcfa-421482d305b6 is a run of 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:47:58+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-gw1/testDockerClean_CRx_STOP0/jobstore kind-_testDockerCleanFn/instance-wpk7s5p1. 781s [2026-01-30T23:47:58+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v1 781s Exit reason: None 781s [2026-01-30T23:47:58+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v2 781s [2026-01-30T23:47:58+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-wpk7s5p1" follows: 781s =========> 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v1 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v1 781s [2026-01-30T23:47:58+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 781s apiDockerCall( 781s ~~~~~~~~~~~~~^ 781s job, 781s ^^^^ 781s ...<6 lines>... 781s privileged=True, 781s ^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:47:58+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:47:58+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v2 with ID kind-_testDockerCleanFn/instance-wpk7s5p1 to 0 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 781s [2026-01-30T23:47:58+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v3 is completely failed 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v3 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil.lib.history] Workflow d2f03a72-8f01-4fce-bcfa-421482d305b6 stopped. Success: False 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_STOP0/jobstore) 781s ------------------------------ Captured log call ------------------------------- 781s INFO  toil.lib.history:history.py:369 Recording workflow creation of d2f03a72-8f01-4fce-bcfa-421482d305b6 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_STOP0/jobstore 781s INFO  toil.lib.history:history.py:399 Workflow d2f03a72-8f01-4fce-bcfa-421482d305b6 is a run of 781s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s 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-gw1/testDockerClean_CRx_STOP0/jobstore kind-_testDockerCleanFn/instance-wpk7s5p1. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v1 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v2 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-wpk7s5p1" follows: 781s =========> 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v1 781s [2026-01-30T23:47:58+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v1 781s [2026-01-30T23:47:58+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 781s apiDockerCall( 781s ~~~~~~~~~~~~~^ 781s job, 781s ^^^^ 781s ...<6 lines>... 781s privileged=True, 781s ^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:47:58+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v2 with ID kind-_testDockerCleanFn/instance-wpk7s5p1 to 0 781s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 781s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v3 is completely failed 781s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 781s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-wpk7s5p1 v3 781s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 781s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 781s INFO  toil.lib.history:history.py:530 Workflow d2f03a72-8f01-4fce-bcfa-421482d305b6 stopped. Success: False 781s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_STOP0/jobstore) 781s ______________________ TestDocker.testDockerClean_CRx_RM _______________________ 781s [gw1] linux -- Python 3.13.11 /usr/bin/python3.13 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 781s toil.start(A) 781s ~~~~~~~~~~^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 781s return self._runMainLoop(rootJobDescription) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 781s ).run() 781s ~~~^^ 781s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 781s raise FailedJobsException( 781s ...<3 lines>... 781s ) 781s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_RM0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v3 781s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v3" follows: 781s =========> 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v1 781s [2026-01-30T23:48:03+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v1 781s [2026-01-30T23:48:03+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq 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. 781s [2026-01-30T23:48:03+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 781s apiDockerCall( 781s ~~~~~~~~~~~~~^ 781s job, 781s ^^^^ 781s ...<6 lines>... 781s privileged=True, 781s ^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:03+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 781s result: TResult | None = func() 781s ~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 781s lambda: runtest_hook(item=item, **kwds), 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 781s yield 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 781s return result.get_result() 781s ~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 781s raise exc.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 781s res = yield 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 781s item.runtest() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 781s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 781s result = testfunction(**testargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 143, in testDockerClean_CRx_RM 781s self.testDockerClean( 781s ~~~~~~~~~~~~~~~~~~~~^ 781s tmp_path, caching=False, detached=False, rm=True, deferParam=RM 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 781s file_stats = test_file.stat() 781s File "/usr/lib/python3.13/pathlib/_local.py", line 517, in stat 781s return os.stat(self, follow_symlinks=follow_symlinks) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_RM0/working/test.txt' 781s ----------------------------- Captured stderr call ----------------------------- 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 3470b0f3-8418-4717-84de-c0e923cafef4 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_RM0/jobstore 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil.lib.history] Workflow 3470b0f3-8418-4717-84de-c0e923cafef4 is a run of 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:48:03+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-gw1/testDockerClean_CRx_RM0/jobstore kind-_testDockerCleanFn/instance-n5ikqwxq. 781s [2026-01-30T23:48:03+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v1 781s Exit reason: None 781s [2026-01-30T23:48:03+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v2 781s [2026-01-30T23:48:03+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-n5ikqwxq" follows: 781s =========> 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v1 781s [2026-01-30T23:48:03+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v1 781s [2026-01-30T23:48:03+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq 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. 781s [2026-01-30T23:48:03+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 781s apiDockerCall( 781s ~~~~~~~~~~~~~^ 781s job, 781s ^^^^ 781s ...<6 lines>... 781s privileged=True, 781s ^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:03+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:48:03+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v2 with ID kind-_testDockerCleanFn/instance-n5ikqwxq to 0 781s [2026-01-30T23:48:03+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 781s [2026-01-30T23:48:03+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v3 is completely failed 781s [2026-01-30T23:48:03+0000] [Thread-17 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:48:03: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq 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. 781s [2026-01-30T23:48:06+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s [2026-01-30T23:48:06+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 781s [2026-01-30T23:48:06+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v3 781s [2026-01-30T23:48:06+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.lib.history] Workflow 3470b0f3-8418-4717-84de-c0e923cafef4 stopped. Success: False 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_RM0/jobstore) 781s ------------------------------ Captured log call ------------------------------- 781s INFO  toil.lib.history:history.py:369 Recording workflow creation of 3470b0f3-8418-4717-84de-c0e923cafef4 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_RM0/jobstore 781s INFO  toil.lib.history:history.py:399 Workflow 3470b0f3-8418-4717-84de-c0e923cafef4 is a run of 781s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s 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-gw1/testDockerClean_CRx_RM0/jobstore kind-_testDockerCleanFn/instance-n5ikqwxq. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v1 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v2 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-n5ikqwxq" follows: 781s =========> 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:02+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v1 781s [2026-01-30T23:48:03+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v1 781s [2026-01-30T23:48:03+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq 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. 781s [2026-01-30T23:48:03+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 781s apiDockerCall( 781s ~~~~~~~~~~~~~^ 781s job, 781s ^^^^ 781s ...<6 lines>... 781s privileged=True, 781s ^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:03+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v2 with ID kind-_testDockerCleanFn/instance-n5ikqwxq to 0 781s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 781s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v3 is completely failed 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:48:03: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq 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. 781s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 781s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-n5ikqwxq v3 781s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 781s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 781s INFO  toil.lib.history:history.py:530 Workflow 3470b0f3-8418-4717-84de-c0e923cafef4 stopped. Success: False 781s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_RM0/jobstore) 781s ________________________ TestDocker.testDockerPipeChain ________________________ 781s [gw1] linux -- Python 3.13.11 /usr/bin/python3.13 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 781s result: TResult | None = func() 781s ~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 781s lambda: runtest_hook(item=item, **kwds), 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 781s yield 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 781s return result.get_result() 781s ~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 781s raise exc.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 781s res = yield 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 781s item.runtest() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 781s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 781s result = testfunction(**testargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 310, in testDockerPipeChain 781s rv = Job.Runner.startToil(A, options) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 781s return toil.start(job) 781s ~~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 781s return self._runMainLoop(rootJobDescription) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 781s ).run() 781s ~~~^^ 781s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 781s raise FailedJobsException( 781s ...<3 lines>... 781s ) 781s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerPipeChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v6 781s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v6" follows: 781s =========> 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v4 781s [2026-01-30T23:48:08+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v4 781s [2026-01-30T23:48:08+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 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. 781s [2026-01-30T23:48:08+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 781s return apiDockerCall( 781s job, 781s ...<2 lines>... 781s privileged=True, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:08+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s ----------------------------- Captured stderr call ----------------------------- 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of c05dc8b1-4a0e-44e2-a182-46c4bd39982a in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerPipeChain0/jobstore 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.lib.history] Workflow c05dc8b1-4a0e-44e2-a182-46c4bd39982a is a run of 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:48:07+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-gw1/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-ev7yp817. 781s [2026-01-30T23:48:07+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v1 781s Exit reason: None 781s [2026-01-30T23:48:07+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v2 781s [2026-01-30T23:48:07+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-ev7yp817" follows: 781s =========> 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v1 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v1 781s [2026-01-30T23:48:07+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 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. 781s [2026-01-30T23:48:07+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 781s return apiDockerCall( 781s job, 781s ...<2 lines>... 781s privileged=True, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:07+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:48:07+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v2 with ID kind-_testDockerPipeChainFn/instance-ev7yp817 to 1 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:48:07+0000] [Thread-21 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:48:07: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 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. 781s [2026-01-30T23:48:08+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-gw1/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-ev7yp817. 781s [2026-01-30T23:48:08+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v3 781s Exit reason: None 781s [2026-01-30T23:48:08+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v5 781s [2026-01-30T23:48:08+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-ev7yp817" follows: 781s =========> 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v4 781s [2026-01-30T23:48:08+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v4 781s [2026-01-30T23:48:08+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 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. 781s [2026-01-30T23:48:08+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 781s return apiDockerCall( 781s job, 781s ...<2 lines>... 781s privileged=True, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:08+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:48:08+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v5 with ID kind-_testDockerPipeChainFn/instance-ev7yp817 to 0 781s [2026-01-30T23:48:08+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v6 is completely failed 781s [2026-01-30T23:48:08+0000] [Thread-21 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:48:08: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 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. 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v6 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.lib.history] Workflow c05dc8b1-4a0e-44e2-a182-46c4bd39982a stopped. Success: False 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerPipeChain0/jobstore) 781s ------------------------------ Captured log call ------------------------------- 781s INFO  toil.lib.history:history.py:369 Recording workflow creation of c05dc8b1-4a0e-44e2-a182-46c4bd39982a in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerPipeChain0/jobstore 781s INFO  toil.lib.history:history.py:399 Workflow c05dc8b1-4a0e-44e2-a182-46c4bd39982a is a run of 781s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s 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-gw1/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-ev7yp817. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v1 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v2 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-ev7yp817" follows: 781s =========> 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v1 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v1 781s [2026-01-30T23:48:07+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 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. 781s [2026-01-30T23:48:07+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 781s return apiDockerCall( 781s job, 781s ...<2 lines>... 781s privileged=True, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:07+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v2 with ID kind-_testDockerPipeChainFn/instance-ev7yp817 to 1 781s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:48:07: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 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. 781s 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-gw1/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-ev7yp817. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v3 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v5 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-ev7yp817" follows: 781s =========> 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v4 781s [2026-01-30T23:48:08+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v4 781s [2026-01-30T23:48:08+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 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. 781s [2026-01-30T23:48:08+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 781s return apiDockerCall( 781s job, 781s ...<2 lines>... 781s privileged=True, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:08+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v5 with ID kind-_testDockerPipeChainFn/instance-ev7yp817 to 0 781s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v6 is completely failed 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:48:08: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 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. 781s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 781s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v6 781s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 781s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 781s INFO  toil.lib.history:history.py:530 Workflow c05dc8b1-4a0e-44e2-a182-46c4bd39982a stopped. Success: False 781s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerPipeChain0/jobstore) 781s _________________ TestDocker.testDockerPipeChainErrorDetection _________________ 781s [gw1] linux -- Python 3.13.11 /usr/bin/python3.13 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 781s result: TResult | None = func() 781s ~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 781s lambda: runtest_hook(item=item, **kwds), 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 781s yield 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 781s return result.get_result() 781s ~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 781s raise exc.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 781s res = yield 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 781s item.runtest() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 781s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 781s result = testfunction(**testargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 332, in testDockerPipeChainErrorDetection 781s rv = Job.Runner.startToil(A, options) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 781s return toil.start(job) 781s ~~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 781s return self._runMainLoop(rootJobDescription) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 781s ).run() 781s ~~~^^ 781s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 781s raise FailedJobsException( 781s ...<3 lines>... 781s ) 781s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerPipeChainErrorDetect0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v6 781s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v6" follows: 781s =========> 781s [2026-01-30T23:48:12+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:12+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:12+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v4 781s [2026-01-30T23:48:12+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v4 781s [2026-01-30T23:48:12+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 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. 781s [2026-01-30T23:48:12+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 781s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 781s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:12+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s ----------------------------- Captured stderr call ----------------------------- 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of d65b5883-8262-443b-9788-69c559c0aeaf in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerPipeChainErrorDetect0/jobstore 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.lib.history] Workflow d65b5883-8262-443b-9788-69c559c0aeaf is a run of 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:48:11+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-gw1/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5. 781s [2026-01-30T23:48:11+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v1 781s Exit reason: None 781s [2026-01-30T23:48:11+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v2 781s [2026-01-30T23:48:11+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5" follows: 781s =========> 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v1 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v1 781s [2026-01-30T23:48:11+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 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. 781s [2026-01-30T23:48:11+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 781s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 781s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:11+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:48:11+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v2 with ID kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 to 1 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:48:11+0000] [Thread-25 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:48:11: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 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. 781s [2026-01-30T23:48:12+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-gw1/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5. 781s [2026-01-30T23:48:12+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v3 781s Exit reason: None 781s [2026-01-30T23:48:12+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v5 781s [2026-01-30T23:48:12+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5" follows: 781s =========> 781s [2026-01-30T23:48:12+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:12+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:12+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v4 781s [2026-01-30T23:48:12+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v4 781s [2026-01-30T23:48:12+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 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. 781s [2026-01-30T23:48:12+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 781s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 781s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:12+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:48:12+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v5 with ID kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 to 0 781s [2026-01-30T23:48:12+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v6 is completely failed 781s [2026-01-30T23:48:12+0000] [Thread-25 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:48:12: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 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. 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v6 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.lib.history] Workflow d65b5883-8262-443b-9788-69c559c0aeaf stopped. Success: False 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerPipeChainErrorDetect0/jobstore) 781s ------------------------------ Captured log call ------------------------------- 781s INFO  toil.lib.history:history.py:369 Recording workflow creation of d65b5883-8262-443b-9788-69c559c0aeaf in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerPipeChainErrorDetect0/jobstore 781s INFO  toil.lib.history:history.py:399 Workflow d65b5883-8262-443b-9788-69c559c0aeaf is a run of 781s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s 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-gw1/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v1 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v2 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5" follows: 781s =========> 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v1 781s [2026-01-30T23:48:11+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v1 781s [2026-01-30T23:48:11+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 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. 781s [2026-01-30T23:48:11+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 781s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 781s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:11+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v2 with ID kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 to 1 781s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:48:11: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 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. 781s 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-gw1/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v3 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v5 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5" follows: 781s =========> 781s [2026-01-30T23:48:12+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:12+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:12+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v4 781s [2026-01-30T23:48:12+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v4 781s [2026-01-30T23:48:12+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 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. 781s [2026-01-30T23:48:12+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 781s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 781s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:12+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v5 with ID kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 to 0 781s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v6 is completely failed 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:48:12: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 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. 781s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 781s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v6 781s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 781s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 781s INFO  toil.lib.history:history.py:530 Workflow d65b5883-8262-443b-9788-69c559c0aeaf stopped. Success: False 781s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerPipeChainErrorDetect0/jobstore) 781s _____________________ TestDocker.testNonCachingDockerChain _____________________ 781s [gw1] linux -- Python 3.13.11 /usr/bin/python3.13 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 781s result: TResult | None = func() 781s ~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 781s lambda: runtest_hook(item=item, **kwds), 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 781s yield 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 781s return result.get_result() 781s ~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 781s raise exc.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 781s res = yield 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 781s item.runtest() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 781s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 781s result = testfunction(**testargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 336, in testNonCachingDockerChain 781s self.testDockerPipeChain(tmp_path, caching=True) 781s ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 310, in testDockerPipeChain 781s rv = Job.Runner.startToil(A, options) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 781s return toil.start(job) 781s ~~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 781s return self._runMainLoop(rootJobDescription) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 781s ).run() 781s ~~~^^ 781s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 781s raise FailedJobsException( 781s ...<3 lines>... 781s ) 781s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testNonCachingDockerChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v6 781s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v6" follows: 781s =========> 781s [2026-01-30T23:48:16+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:16+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:16+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v4 781s [2026-01-30T23:48:16+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v4 781s [2026-01-30T23:48:16+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r 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. 781s [2026-01-30T23:48:16+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 781s return apiDockerCall( 781s job, 781s ...<2 lines>... 781s privileged=True, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:16+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s ----------------------------- Captured stderr call ----------------------------- 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 2fbb06b8-6ac1-4f3f-b9a3-95bf46c419bd in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testNonCachingDockerChain0/jobstore 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.lib.history] Workflow 2fbb06b8-6ac1-4f3f-b9a3-95bf46c419bd is a run of 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:48:15+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-gw1/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-uup2z07r. 781s [2026-01-30T23:48:15+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v1 781s Exit reason: None 781s [2026-01-30T23:48:15+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v2 781s [2026-01-30T23:48:15+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-uup2z07r" follows: 781s =========> 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v1 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v1 781s [2026-01-30T23:48:15+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r 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. 781s [2026-01-30T23:48:15+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 781s return apiDockerCall( 781s job, 781s ...<2 lines>... 781s privileged=True, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:15+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:48:15+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v2 with ID kind-_testDockerPipeChainFn/instance-uup2z07r to 1 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:48:15+0000] [Thread-29 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:48:15: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r 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. 781s [2026-01-30T23:48:16+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-gw1/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-uup2z07r. 781s [2026-01-30T23:48:16+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v3 781s Exit reason: None 781s [2026-01-30T23:48:16+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v5 781s [2026-01-30T23:48:16+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-uup2z07r" follows: 781s =========> 781s [2026-01-30T23:48:16+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:16+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:16+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v4 781s [2026-01-30T23:48:16+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v4 781s [2026-01-30T23:48:16+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r 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. 781s [2026-01-30T23:48:16+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 781s return apiDockerCall( 781s job, 781s ...<2 lines>... 781s privileged=True, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:16+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:48:16+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v5 with ID kind-_testDockerPipeChainFn/instance-uup2z07r to 0 781s [2026-01-30T23:48:16+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v6 is completely failed 781s [2026-01-30T23:48:16+0000] [Thread-29 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:48:16: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r 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. 781s [2026-01-30T23:48:19+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s [2026-01-30T23:48:19+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 781s [2026-01-30T23:48:19+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v6 781s [2026-01-30T23:48:19+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 781s [2026-01-30T23:48:19+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 781s [2026-01-30T23:48:19+0000] [MainThread] [I] [toil.lib.history] Workflow 2fbb06b8-6ac1-4f3f-b9a3-95bf46c419bd stopped. Success: False 781s [2026-01-30T23:48:19+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testNonCachingDockerChain0/jobstore) 781s ------------------------------ Captured log call ------------------------------- 781s INFO  toil.lib.history:history.py:369 Recording workflow creation of 2fbb06b8-6ac1-4f3f-b9a3-95bf46c419bd in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testNonCachingDockerChain0/jobstore 781s INFO  toil.lib.history:history.py:399 Workflow 2fbb06b8-6ac1-4f3f-b9a3-95bf46c419bd is a run of 781s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s 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-gw1/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-uup2z07r. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v1 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v2 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-uup2z07r" follows: 781s =========> 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v1 781s [2026-01-30T23:48:15+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v1 781s [2026-01-30T23:48:15+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r 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. 781s [2026-01-30T23:48:15+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 781s return apiDockerCall( 781s job, 781s ...<2 lines>... 781s privileged=True, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:15+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v2 with ID kind-_testDockerPipeChainFn/instance-uup2z07r to 1 781s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:48:15: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r 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. 781s 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-gw1/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-uup2z07r. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v3 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v5 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-uup2z07r" follows: 781s =========> 781s [2026-01-30T23:48:16+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:16+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:16+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v4 781s [2026-01-30T23:48:16+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v4 781s [2026-01-30T23:48:16+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r 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. 781s [2026-01-30T23:48:16+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 781s return apiDockerCall( 781s job, 781s ...<2 lines>... 781s privileged=True, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:16+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v5 with ID kind-_testDockerPipeChainFn/instance-uup2z07r to 0 781s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v6 is completely failed 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:48:16: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r 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. 781s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 781s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v6 781s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 781s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 781s INFO  toil.lib.history:history.py:530 Workflow 2fbb06b8-6ac1-4f3f-b9a3-95bf46c419bd stopped. Success: False 781s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testNonCachingDockerChain0/jobstore) 781s ______________ TestDocker.testNonCachingDockerChainErrorDetection ______________ 781s [gw1] linux -- Python 3.13.11 /usr/bin/python3.13 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 781s result: TResult | None = func() 781s ~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 781s lambda: runtest_hook(item=item, **kwds), 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 781s yield 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 781s return result.get_result() 781s ~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 781s raise exc.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 781s res = yield 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 781s item.runtest() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 781s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 781s result = testfunction(**testargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 339, in testNonCachingDockerChainErrorDetection 781s self.testDockerPipeChainErrorDetection(tmp_path, caching=True) 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 332, in testDockerPipeChainErrorDetection 781s rv = Job.Runner.startToil(A, options) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 781s return toil.start(job) 781s ~~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 781s return self._runMainLoop(rootJobDescription) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 781s ).run() 781s ~~~^^ 781s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 781s raise FailedJobsException( 781s ...<3 lines>... 781s ) 781s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testNonCachingDockerChainError0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v6 781s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v6" follows: 781s =========> 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v4 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v4 781s [2026-01-30T23:48:20+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd 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. 781s [2026-01-30T23:48:20+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 781s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 781s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:20+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s ----------------------------- Captured stderr call ----------------------------- 781s [2026-01-30T23:48:19+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of a6746162-599c-4583-80e4-7106ccd3e730 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testNonCachingDockerChainError0/jobstore 781s [2026-01-30T23:48:19+0000] [MainThread] [I] [toil.lib.history] Workflow a6746162-599c-4583-80e4-7106ccd3e730 is a run of 781s [2026-01-30T23:48:19+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:19+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 781s [2026-01-30T23:48:19+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:48:20+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-gw1/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-cpncgngd. 781s [2026-01-30T23:48:20+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v1 781s Exit reason: None 781s [2026-01-30T23:48:20+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v2 781s [2026-01-30T23:48:20+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-cpncgngd" follows: 781s =========> 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v1 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v1 781s [2026-01-30T23:48:20+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd 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. 781s [2026-01-30T23:48:20+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 781s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 781s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:20+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:48:20+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v2 with ID kind-_testDockerPipeChainErrorFn/instance-cpncgngd to 1 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:48:20+0000] [Thread-33 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:48:20: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd 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. 781s [2026-01-30T23:48:20+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-gw1/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-cpncgngd. 781s [2026-01-30T23:48:20+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v3 781s Exit reason: None 781s [2026-01-30T23:48:20+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v5 781s [2026-01-30T23:48:20+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-cpncgngd" follows: 781s =========> 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v4 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v4 781s [2026-01-30T23:48:20+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd 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. 781s [2026-01-30T23:48:20+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 781s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 781s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:20+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:48:20+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v5 with ID kind-_testDockerPipeChainErrorFn/instance-cpncgngd to 0 781s [2026-01-30T23:48:20+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v6 is completely failed 781s [2026-01-30T23:48:20+0000] [Thread-33 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:48:20: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd 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. 781s [2026-01-30T23:48:24+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s [2026-01-30T23:48:24+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 781s [2026-01-30T23:48:24+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v6 781s [2026-01-30T23:48:24+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 781s [2026-01-30T23:48:24+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 781s [2026-01-30T23:48:25+0000] [MainThread] [I] [toil.lib.history] Workflow a6746162-599c-4583-80e4-7106ccd3e730 stopped. Success: False 781s [2026-01-30T23:48:25+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testNonCachingDockerChainError0/jobstore) 781s ------------------------------ Captured log call ------------------------------- 781s INFO  toil.lib.history:history.py:369 Recording workflow creation of a6746162-599c-4583-80e4-7106ccd3e730 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testNonCachingDockerChainError0/jobstore 781s INFO  toil.lib.history:history.py:399 Workflow a6746162-599c-4583-80e4-7106ccd3e730 is a run of 781s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s 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-gw1/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-cpncgngd. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v1 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v2 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-cpncgngd" follows: 781s =========> 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v1 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v1 781s [2026-01-30T23:48:20+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd 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. 781s [2026-01-30T23:48:20+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 781s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 781s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:20+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v2 with ID kind-_testDockerPipeChainErrorFn/instance-cpncgngd to 1 781s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:48:20: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd 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. 781s 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-gw1/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-cpncgngd. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v3 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v5 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-cpncgngd" follows: 781s =========> 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v4 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v4 781s [2026-01-30T23:48:20+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd 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. 781s [2026-01-30T23:48:20+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 781s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 781s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:20+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v5 with ID kind-_testDockerPipeChainErrorFn/instance-cpncgngd to 0 781s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v6 is completely failed 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:48:20: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd 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. 781s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 781s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v6 781s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 781s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 781s INFO  toil.lib.history:history.py:530 Workflow a6746162-599c-4583-80e4-7106ccd3e730 stopped. Success: False 781s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testNonCachingDockerChainError0/jobstore) 781s __________________________ TestDocker.testDockerLogs ___________________________ 781s [gw1] linux -- Python 3.13.11 /usr/bin/python3.13 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 781s result: TResult | None = func() 781s ~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 781s lambda: runtest_hook(item=item, **kwds), 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 781s yield 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 781s return result.get_result() 781s ~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 781s raise exc.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 781s res = yield 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 781s item.runtest() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 781s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 781s result = testfunction(**testargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 781s rv = Job.Runner.startToil(A, options) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 781s return toil.start(job) 781s ~~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 781s return self._runMainLoop(rootJobDescription) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 781s ).run() 781s ~~~^^ 781s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 781s raise FailedJobsException( 781s ...<3 lines>... 781s ) 781s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v6 781s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v6" follows: 781s =========> 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v4 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v4 781s [2026-01-30T23:48:26+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r 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. 781s [2026-01-30T23:48:26+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:26+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s ----------------------------- Captured stderr call ----------------------------- 781s [2026-01-30T23:48:25+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 233af8b4-8a5c-48bd-8f1b-f9d608b9208d in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs0/jobstore 781s [2026-01-30T23:48:25+0000] [MainThread] [I] [toil.lib.history] Workflow 233af8b4-8a5c-48bd-8f1b-f9d608b9208d is a run of 781s [2026-01-30T23:48:25+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:25+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 781s [2026-01-30T23:48:25+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:48:26+0000] [Thread-37 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:48:26: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r 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. 781s [2026-01-30T23:48:26+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-gw1/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-r15esd0r. 781s [2026-01-30T23:48:26+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v1 781s Exit reason: None 781s [2026-01-30T23:48:26+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v2 781s [2026-01-30T23:48:26+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-r15esd0r" follows: 781s =========> 781s [2026-01-30T23:48:25+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:25+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:25+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v1 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v1 781s [2026-01-30T23:48:26+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r 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. 781s [2026-01-30T23:48:26+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:26+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:48:26+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v2 with ID kind-_testDockerLogsFn/instance-r15esd0r to 1 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:48:26+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-gw1/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-r15esd0r. 781s [2026-01-30T23:48:26+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v3 781s Exit reason: None 781s [2026-01-30T23:48:26+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v5 781s [2026-01-30T23:48:26+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-r15esd0r" follows: 781s =========> 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v4 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v4 781s [2026-01-30T23:48:26+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r 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. 781s [2026-01-30T23:48:26+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:26+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:48:26+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v5 with ID kind-_testDockerLogsFn/instance-r15esd0r to 0 781s [2026-01-30T23:48:26+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v6 is completely failed 781s [2026-01-30T23:48:26+0000] [Thread-37 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:48:26: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r 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. 781s [2026-01-30T23:48:30+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s [2026-01-30T23:48:30+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 781s [2026-01-30T23:48:30+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v6 781s [2026-01-30T23:48:30+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.lib.history] Workflow 233af8b4-8a5c-48bd-8f1b-f9d608b9208d stopped. Success: False 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs0/jobstore) 781s ------------------------------ Captured log call ------------------------------- 781s INFO  toil.lib.history:history.py:369 Recording workflow creation of 233af8b4-8a5c-48bd-8f1b-f9d608b9208d in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs0/jobstore 781s INFO  toil.lib.history:history.py:399 Workflow 233af8b4-8a5c-48bd-8f1b-f9d608b9208d is a run of 781s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:48:26: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r 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. 781s 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-gw1/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-r15esd0r. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v1 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v2 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-r15esd0r" follows: 781s =========> 781s [2026-01-30T23:48:25+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:25+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:25+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v1 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v1 781s [2026-01-30T23:48:26+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r 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. 781s [2026-01-30T23:48:26+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:26+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v2 with ID kind-_testDockerLogsFn/instance-r15esd0r to 1 781s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s 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-gw1/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-r15esd0r. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v3 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v5 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-r15esd0r" follows: 781s =========> 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v4 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v4 781s [2026-01-30T23:48:26+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r 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. 781s [2026-01-30T23:48:26+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:26+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v5 with ID kind-_testDockerLogsFn/instance-r15esd0r to 0 781s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v6 is completely failed 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:48:26: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r 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. 781s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 781s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v6 781s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 781s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 781s INFO  toil.lib.history:history.py:530 Workflow 233af8b4-8a5c-48bd-8f1b-f9d608b9208d stopped. Success: False 781s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs0/jobstore) 781s _______________________ TestDocker.testDockerLogs_Stream _______________________ 781s [gw1] linux -- Python 3.13.11 /usr/bin/python3.13 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 781s result: TResult | None = func() 781s ~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 781s lambda: runtest_hook(item=item, **kwds), 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 781s yield 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 781s return result.get_result() 781s ~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 781s raise exc.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 781s res = yield 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 781s item.runtest() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 781s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 781s result = testfunction(**testargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 366, in testDockerLogs_Stream 781s self.testDockerLogs(tmp_path, stream=True, demux=False) 781s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 781s rv = Job.Runner.startToil(A, options) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 781s return toil.start(job) 781s ~~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 781s return self._runMainLoop(rootJobDescription) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 781s ).run() 781s ~~~^^ 781s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 781s raise FailedJobsException( 781s ...<3 lines>... 781s ) 781s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v6 781s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v6" follows: 781s =========> 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v4 781s [2026-01-30T23:48:32+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v4 781s [2026-01-30T23:48:32+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g 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. 781s [2026-01-30T23:48:32+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:32+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s ----------------------------- Captured stderr call ----------------------------- 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 68b1acad-d03a-4b06-98d6-be303f4833b6 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Stream0/jobstore 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.lib.history] Workflow 68b1acad-d03a-4b06-98d6-be303f4833b6 is a run of 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:48:31+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-gw1/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-d1ho2z3g. 781s [2026-01-30T23:48:31+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v1 781s Exit reason: None 781s [2026-01-30T23:48:31+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v2 781s [2026-01-30T23:48:31+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-d1ho2z3g" follows: 781s =========> 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v1 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v1 781s [2026-01-30T23:48:31+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g 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. 781s [2026-01-30T23:48:31+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:31+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:48:31+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v2 with ID kind-_testDockerLogsFn/instance-d1ho2z3g to 1 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:48:31+0000] [Thread-41 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:48:31: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g 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. 781s [2026-01-30T23:48:32+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-gw1/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-d1ho2z3g. 781s [2026-01-30T23:48:32+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v3 781s Exit reason: None 781s [2026-01-30T23:48:32+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v5 781s [2026-01-30T23:48:32+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-d1ho2z3g" follows: 781s =========> 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v4 781s [2026-01-30T23:48:32+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v4 781s [2026-01-30T23:48:32+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g 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. 781s [2026-01-30T23:48:32+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:32+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:48:32+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v5 with ID kind-_testDockerLogsFn/instance-d1ho2z3g to 0 781s [2026-01-30T23:48:32+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v6 is completely failed 781s [2026-01-30T23:48:32+0000] [Thread-41 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:48:32: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g 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. 781s [2026-01-30T23:48:35+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/fE: pybuild pybuild:483: test: plugin pyproject failed with: exit code=1: cd /tmp/autopkgtest.IiScC1/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 781s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.14 3.13" returned exit code 13 781s make: *** [/tmp/jlGsUxPO0b/run:4: pybuild-autopkgtest] Error 25 781s pybuild-autopkgtest: error: /tmp/jlGsUxPO0b/run pybuild-autopkgtest returned exit code 2 781s ailed.log... 781s [2026-01-30T23:48:35+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 781s [2026-01-30T23:48:35+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v6 781s [2026-01-30T23:48:35+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 781s [2026-01-30T23:48:35+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 781s [2026-01-30T23:48:35+0000] [MainThread] [I] [toil.lib.history] Workflow 68b1acad-d03a-4b06-98d6-be303f4833b6 stopped. Success: False 781s [2026-01-30T23:48:35+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Stream0/jobstore) 781s ------------------------------ Captured log call ------------------------------- 781s INFO  toil.lib.history:history.py:369 Recording workflow creation of 68b1acad-d03a-4b06-98d6-be303f4833b6 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Stream0/jobstore 781s INFO  toil.lib.history:history.py:399 Workflow 68b1acad-d03a-4b06-98d6-be303f4833b6 is a run of 781s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s 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-gw1/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-d1ho2z3g. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v1 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v2 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-d1ho2z3g" follows: 781s =========> 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v1 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v1 781s [2026-01-30T23:48:31+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g 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. 781s [2026-01-30T23:48:31+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:31+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v2 with ID kind-_testDockerLogsFn/instance-d1ho2z3g to 1 781s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:48:31: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g 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. 781s 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-gw1/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-d1ho2z3g. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v3 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v5 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-d1ho2z3g" follows: 781s =========> 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v4 781s [2026-01-30T23:48:32+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v4 781s [2026-01-30T23:48:32+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g 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. 781s [2026-01-30T23:48:32+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:32+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v5 with ID kind-_testDockerLogsFn/instance-d1ho2z3g to 0 781s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v6 is completely failed 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:48:32: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g 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. 781s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 781s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v6 781s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 781s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 781s INFO  toil.lib.history:history.py:530 Workflow 68b1acad-d03a-4b06-98d6-be303f4833b6 stopped. Success: False 781s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Stream0/jobstore) 781s _______________________ TestDocker.testDockerLogs_Demux ________________________ 781s [gw1] linux -- Python 3.13.11 /usr/bin/python3.13 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 781s result: TResult | None = func() 781s ~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 781s lambda: runtest_hook(item=item, **kwds), 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 781s yield 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 781s return result.get_result() 781s ~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 781s raise exc.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 781s res = yield 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 781s item.runtest() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 781s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 781s result = testfunction(**testargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 369, in testDockerLogs_Demux 781s self.testDockerLogs(tmp_path, stream=False, demux=True) 781s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 781s rv = Job.Runner.startToil(A, options) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 781s return toil.start(job) 781s ~~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 781s return self._runMainLoop(rootJobDescription) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 781s ).run() 781s ~~~^^ 781s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 781s raise FailedJobsException( 781s ...<3 lines>... 781s ) 781s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Demux0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v6 781s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v6" follows: 781s =========> 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v4 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v4 781s [2026-01-30T23:48:36+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu 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. 781s [2026-01-30T23:48:36+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:36+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s ----------------------------- Captured stderr call ----------------------------- 781s [2026-01-30T23:48:35+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of efb1e83a-090c-4f3c-ba07-ab847ede6c76 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Demux0/jobstore 781s [2026-01-30T23:48:35+0000] [MainThread] [I] [toil.lib.history] Workflow efb1e83a-090c-4f3c-ba07-ab847ede6c76 is a run of 781s [2026-01-30T23:48:35+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:35+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 781s [2026-01-30T23:48:35+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:48:36+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-gw1/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-2we6n_wu. 781s [2026-01-30T23:48:36+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v1 781s Exit reason: None 781s [2026-01-30T23:48:36+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v2 781s [2026-01-30T23:48:36+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-2we6n_wu" follows: 781s =========> 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v1 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v1 781s [2026-01-30T23:48:36+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu 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. 781s [2026-01-30T23:48:36+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:36+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:48:36+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v2 with ID kind-_testDockerLogsFn/instance-2we6n_wu to 1 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:48:36+0000] [Thread-45 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:48:36: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu 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. 781s [2026-01-30T23:48:36+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-gw1/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-2we6n_wu. 781s [2026-01-30T23:48:36+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v3 781s Exit reason: None 781s [2026-01-30T23:48:36+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v5 781s [2026-01-30T23:48:36+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-2we6n_wu" follows: 781s =========> 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v4 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v4 781s [2026-01-30T23:48:36+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu 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. 781s [2026-01-30T23:48:36+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:36+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:48:36+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v5 with ID kind-_testDockerLogsFn/instance-2we6n_wu to 0 781s [2026-01-30T23:48:36+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v6 is completely failed 781s [2026-01-30T23:48:36+0000] [Thread-45 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:48:36: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu 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. 781s [2026-01-30T23:48:39+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s [2026-01-30T23:48:39+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 781s [2026-01-30T23:48:39+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v6 781s [2026-01-30T23:48:39+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 781s [2026-01-30T23:48:39+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 781s [2026-01-30T23:48:39+0000] [MainThread] [I] [toil.lib.history] Workflow efb1e83a-090c-4f3c-ba07-ab847ede6c76 stopped. Success: False 781s [2026-01-30T23:48:39+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Demux0/jobstore) 781s ------------------------------ Captured log call ------------------------------- 781s INFO  toil.lib.history:history.py:369 Recording workflow creation of efb1e83a-090c-4f3c-ba07-ab847ede6c76 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Demux0/jobstore 781s INFO  toil.lib.history:history.py:399 Workflow efb1e83a-090c-4f3c-ba07-ab847ede6c76 is a run of 781s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s 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-gw1/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-2we6n_wu. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v1 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v2 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-2we6n_wu" follows: 781s =========> 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v1 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v1 781s [2026-01-30T23:48:36+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu 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. 781s [2026-01-30T23:48:36+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:36+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v2 with ID kind-_testDockerLogsFn/instance-2we6n_wu to 1 781s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:48:36: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu 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. 781s 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-gw1/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-2we6n_wu. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v3 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v5 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-2we6n_wu" follows: 781s =========> 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v4 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v4 781s [2026-01-30T23:48:36+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu 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. 781s [2026-01-30T23:48:36+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:36+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v5 with ID kind-_testDockerLogsFn/instance-2we6n_wu to 0 781s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v6 is completely failed 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:48:36: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu 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. 781s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 781s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v6 781s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 781s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 781s INFO  toil.lib.history:history.py:530 Workflow efb1e83a-090c-4f3c-ba07-ab847ede6c76 stopped. Success: False 781s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Demux0/jobstore) 781s ____________________ TestDocker.testDockerLogs_Demux_Stream ____________________ 781s [gw1] linux -- Python 3.13.11 /usr/bin/python3.13 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 781s result: TResult | None = func() 781s ~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 781s lambda: runtest_hook(item=item, **kwds), 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 781s yield 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 781s return result.get_result() 781s ~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 781s raise exc.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 781s res = yield 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 781s teardown.throw(exception) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 781s return (yield) 781s ^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 781s item.runtest() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 781s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 781s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 781s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 781s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 781s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 781s raise exception 781s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 781s res = hook_impl.function(*args) 781s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 781s result = testfunction(**testargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 372, in testDockerLogs_Demux_Stream 781s self.testDockerLogs(tmp_path, stream=True, demux=True) 781s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 781s rv = Job.Runner.startToil(A, options) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 781s return toil.start(job) 781s ~~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 781s return self._runMainLoop(rootJobDescription) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 781s ).run() 781s ~~~^^ 781s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 781s raise FailedJobsException( 781s ...<3 lines>... 781s ) 781s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Demux_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v6 781s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v6" follows: 781s =========> 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v4 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v4 781s [2026-01-30T23:48:40+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx 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. 781s [2026-01-30T23:48:40+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:40+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s ----------------------------- Captured stderr call ----------------------------- 781s [2026-01-30T23:48:39+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 3e70a3c8-e100-44a0-ab5b-e38957fe9426 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Demux_Stream0/jobstore 781s [2026-01-30T23:48:39+0000] [MainThread] [I] [toil.lib.history] Workflow 3e70a3c8-e100-44a0-ab5b-e38957fe9426 is a run of 781s [2026-01-30T23:48:39+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:39+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 781s [2026-01-30T23:48:39+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:48:40+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-gw1/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-phccplzx. 781s [2026-01-30T23:48:40+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v1 781s Exit reason: None 781s [2026-01-30T23:48:40+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v2 781s [2026-01-30T23:48:40+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-phccplzx" follows: 781s =========> 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v1 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v1 781s [2026-01-30T23:48:40+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:40+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:48:40+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v2 with ID kind-_testDockerLogsFn/instance-phccplzx to 1 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:48:40+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-gw1/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-phccplzx. 781s [2026-01-30T23:48:40+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v3 781s Exit reason: None 781s [2026-01-30T23:48:40+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v5 781s [2026-01-30T23:48:40+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-phccplzx" follows: 781s =========> 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v4 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v4 781s [2026-01-30T23:48:40+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx 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. 781s [2026-01-30T23:48:40+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:40+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:48:40+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v5 with ID kind-_testDockerLogsFn/instance-phccplzx to 0 781s [2026-01-30T23:48:40+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v6 is completely failed 781s [2026-01-30T23:48:40+0000] [Thread-49 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:48:40: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx 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. 781s [2026-01-30T23:48:43+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s [2026-01-30T23:48:43+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 781s [2026-01-30T23:48:43+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v6 781s [2026-01-30T23:48:43+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 781s [2026-01-30T23:48:44+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 781s [2026-01-30T23:48:44+0000] [MainThread] [I] [toil.lib.history] Workflow 3e70a3c8-e100-44a0-ab5b-e38957fe9426 stopped. Success: False 781s [2026-01-30T23:48:44+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Demux_Stream0/jobstore) 781s ------------------------------ Captured log call ------------------------------- 781s INFO  toil.lib.history:history.py:369 Recording workflow creation of 3e70a3c8-e100-44a0-ab5b-e38957fe9426 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Demux_Stream0/jobstore 781s INFO  toil.lib.history:history.py:399 Workflow 3e70a3c8-e100-44a0-ab5b-e38957fe9426 is a run of 781s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s 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-gw1/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-phccplzx. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v1 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v2 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-phccplzx" follows: 781s =========> 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v1 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v1 781s [2026-01-30T23:48:40+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:40+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v2 with ID kind-_testDockerLogsFn/instance-phccplzx to 1 781s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 781s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s 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-gw1/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-phccplzx. 781s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v3 781s Exit reason: None 781s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v5 781s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-phccplzx" follows: 781s =========> 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v4 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v4 781s [2026-01-30T23:48:40+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx 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. 781s [2026-01-30T23:48:40+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:40+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v5 with ID kind-_testDockerLogsFn/instance-phccplzx to 0 781s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v6 is completely failed 781s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 23:48:40: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx 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. 781s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 781s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v6 781s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 781s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 781s INFO  toil.lib.history:history.py:530 Workflow 3e70a3c8-e100-44a0-ab5b-e38957fe9426 stopped. Success: False 781s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Demux_Stream0/jobstore) 781s =========================== short test summary info ============================ 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:603: Configure AWS credentials to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:217: Configure AWS credentials to include this test. 781s 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. 781s 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. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:189: Configure AWS credentials to include this test. 781s 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. 781s 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. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1115: Configure AWS credentials to include this test. 781s 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. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1127: Configure AWS credentials to include this test. 781s 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. 781s 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. 781s 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. 781s 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. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:621: Configure AWS credentials to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:825: Configure AWS credentials to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:800: Configure AWS credentials to include this test. 781s 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. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:151: Configure AWS credentials to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:160: Configure AWS credentials to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:313: Configure AWS credentials to include this test. 781s 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. 781s 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. 781s 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. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:202: Configure AWS credentials to include this test. 781s 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. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1467: Configure AWS credentials to include this test. 781s 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. 781s 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. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1446: Configure AWS credentials to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1079: Configure AWS credentials to include this test. 781s 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. 781s 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. 781s 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. 781s 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. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:450: Configure AWS credentials to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:238: Configure AWS credentials to include this test. 781s 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. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:421: Configure AWS credentials to include this test. 781s 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. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:405: Configure AWS credentials to include this test. 781s 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. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:380: Configure AWS credentials to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:529: Configure AWS credentials to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:264: Configure AWS credentials to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:585: Configure AWS credentials to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:960: Configure AWS credentials to include this test. 781s SKIPPED [13] ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py:1139: Configure AWS credentials to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:32: Consumes unauthenticated Docker Hub pulls if run 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:38: Consumes unauthenticated Docker Hub pulls if run 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:45: Consumes unauthenticated Docker Hub pulls if run 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:26: Consumes unauthenticated Docker Hub pulls if run 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:731: Install Toil with the 'server' extra to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:646: Install Toil with the 'server' extra to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:697: Install Toil with the 'server' extra to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:706: Install Toil with the 'server' extra to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:685: Install Toil with the 'server' extra to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:676: Install Toil with the 'server' extra to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:721: Install Toil with the 'server' extra to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:619: Install Toil with the 'server' extra to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:600: Install Toil with the 'server' extra to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:668: Install Toil with the 'server' extra to include this test. 781s 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. 781s 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. 781s 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. 781s 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. 781s 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. 781s 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. 781s 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. 781s 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. 781s 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. 781s 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. 781s SKIPPED [7] ../../../../usr/lib/python3/dist-packages/_pytest/unittest.py:498: Configure AWS credentials to include this test. 781s 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. 781s 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. 781s 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. 781s 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. 781s 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. 781s 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. 781s 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. 781s 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. 781s 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. 781s 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. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:541: Install Toil with the 'server' extra to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:535: Install Toil with the 'server' extra to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:526: Install Toil with the 'server' extra to include this test. 781s 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. 781s 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. 781s 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. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py:255: Install Toil with the 'wdl' extra to include this test. 781s SKIPPED [3] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:96: Install Toil with the 'server' extra to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:245: Install Toil with the 'server' extra to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1568: Configure AWS credentials to include this test. 781s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:48: Install Toil with the 'server' extra to include this test. 781s FAILED lib/dockerTest.py::TestDocker::testDockerClean - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean0/working/test.txt' 781s FAILED docs/scriptsTest.py::ToilDocumentationTest::testDocker - RuntimeError: [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of adbfe9cd-77b8-4e6c-bcca-28b3dd2ed937 in file:/tmp/tmpsmktma36tutorial_docker 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.lib.history] Workflow adbfe9cd-77b8-4e6c-bcca-28b3dd2ed937 is a run of /usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:47:52+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmpsmktma36tutorial_docker kind-apiDockerCall/instance-tdpmx00b. 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v1 781s Exit reason: None 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v2 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-tdpmx00b" follows: 781s =========> 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v1 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v1) from description 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v1 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b 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. 781s [2026-01-30T23:47:52+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:47:52+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v2 with ID kind-apiDockerCall/instance-tdpmx00b to 1 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 781s [2026-01-30T23:47:52+0000] [Thread-4 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:47:52: Job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b 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. 781s [2026-01-30T23:47:52+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmpsmktma36tutorial_docker kind-apiDockerCall/instance-tdpmx00b. 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v3 781s Exit reason: None 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v5 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-tdpmx00b" follows: 781s =========> 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v4 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v4) from description 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v4 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b 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. 781s [2026-01-30T23:47:52+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:47:52+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v5 with ID kind-apiDockerCall/instance-tdpmx00b to 0 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.leader] Job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v6 is completely failed 781s [2026-01-30T23:47:53+0000] [Thread-4 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 23:47:53: Job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b 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. 781s [2026-01-30T23:47:56+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.IiScC1/autopkgtest_tmp/build/failed.log... 781s [2026-01-30T23:47:56+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 781s [2026-01-30T23:47:56+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v6 781s [2026-01-30T23:47:56+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 781s [2026-01-30T23:47:56+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 781s [2026-01-30T23:47:56+0000] [MainThread] [I] [toil.lib.history] Workflow adbfe9cd-77b8-4e6c-bcca-28b3dd2ed937 stopped. Success: False 781s [2026-01-30T23:47:56+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/tmpsmktma36tutorial_docker) 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py", line 20, in 781s toil.start(align) 781s ~~~~~~~~~~^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 781s return self._runMainLoop(rootJobDescription) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 781s ).run() 781s ~~~^^ 781s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 781s raise FailedJobsException( 781s ...<3 lines>... 781s ) 781s toil.exceptions.FailedJobsException: The job store '/tmp/tmpsmktma36tutorial_docker' contains 1 failed jobs: 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v6 781s Log from job "'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v6" follows: 781s =========> 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v4 781s [2026-01-30T23:47:52+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v4) from description 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b v4 781s [2026-01-30T23:47:52+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'apiDockerCall' kind-apiDockerCall/instance-tdpmx00b 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. 781s [2026-01-30T23:47:52+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:47:52+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_FORGO - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_FORGO0/working/test.txt' 781s FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_STOP - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_STOP0/working/test.txt' 781s FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_RM - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerClean_CRx_RM0/working/test.txt' 781s FAILED lib/dockerTest.py::TestDocker::testDockerPipeChain - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerPipeChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v6 781s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v6" follows: 781s =========> 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:07+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v4 781s [2026-01-30T23:48:08+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 v4 781s [2026-01-30T23:48:08+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-ev7yp817 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. 781s [2026-01-30T23:48:08+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 781s return apiDockerCall( 781s job, 781s ...<2 lines>... 781s privileged=True, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:08+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s FAILED lib/dockerTest.py::TestDocker::testDockerPipeChainErrorDetection - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerPipeChainErrorDetect0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v6 781s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v6" follows: 781s =========> 781s [2026-01-30T23:48:12+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:12+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:12+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v4 781s [2026-01-30T23:48:12+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 v4 781s [2026-01-30T23:48:12+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-w_7j4jm5 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. 781s [2026-01-30T23:48:12+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 781s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 781s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:12+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChain - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testNonCachingDockerChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v6 781s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v6" follows: 781s =========> 781s [2026-01-30T23:48:16+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:16+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:16+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v4 781s [2026-01-30T23:48:16+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r v4 781s [2026-01-30T23:48:16+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-uup2z07r 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. 781s [2026-01-30T23:48:16+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 781s return apiDockerCall( 781s job, 781s ...<2 lines>... 781s privileged=True, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:16+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChainErrorDetection - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testNonCachingDockerChainError0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v6 781s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v6" follows: 781s =========> 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v4 781s [2026-01-30T23:48:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd v4 781s [2026-01-30T23:48:20+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-cpncgngd 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. 781s [2026-01-30T23:48:20+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 781s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 781s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:20+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s FAILED lib/dockerTest.py::TestDocker::testDockerLogs - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v6 781s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v6" follows: 781s =========> 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v4 781s [2026-01-30T23:48:26+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r v4 781s [2026-01-30T23:48:26+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-r15esd0r 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. 781s [2026-01-30T23:48:26+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:26+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Stream - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v6 781s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v6" follows: 781s =========> 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:31+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v4 781s [2026-01-30T23:48:32+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g v4 781s [2026-01-30T23:48:32+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-d1ho2z3g 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. 781s [2026-01-30T23:48:32+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:32+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Demux0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v6 781s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v6" follows: 781s =========> 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v4 781s [2026-01-30T23:48:36+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu v4 781s [2026-01-30T23:48:36+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-2we6n_wu 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. 781s [2026-01-30T23:48:36+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:36+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux_Stream - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw1/testDockerLogs_Demux_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v6 781s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v6" follows: 781s =========> 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v4 781s [2026-01-30T23:48:40+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx v4 781s [2026-01-30T23:48:40+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-phccplzx 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. 781s [2026-01-30T23:48:40+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s PermissionError: [Errno 13] Permission denied 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 781s resp = conn.urlopen( 781s method=request.method, 781s ...<9 lines>... 781s chunked=chunked, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 781s retries = retries.increment( 781s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 781s raise reraise(type(error), error, _stacktrace) 781s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 781s raise value.with_traceback(tb) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 781s response = self._make_request( 781s conn, 781s ...<10 lines>... 781s **response_kw, 781s ) 781s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 781s conn.request( 781s ~~~~~~~~~~~~^ 781s method, 781s ^^^^^^^ 781s ...<6 lines>... 781s enforce_content_length=enforce_content_length, 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 781s self.endheaders() 781s ~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 781s self._send_output(message_body, encode_chunked=encode_chunked) 781s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 781s self.send(msg) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3.13/http/client.py", line 1057, in send 781s self.connect() 781s ~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 781s sock.connect(self.unix_socket) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 781s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s During handling of the above exception, another exception occurred: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 781s return self.version(api_version=False)["ApiVersion"] 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 781s return self._result(self._get(url), json=True) 781s ~~~~~~~~~^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 781s return f(self, *args, **kwargs) 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 781s return self.get(url, **self._set_request_timeout(kwargs)) 781s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 781s return self.request("GET", url, **kwargs) 781s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 781s resp = self.send(prep, **send_kwargs) 781s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 781s r = adapter.send(request, **kwargs) 781s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 781s raise ConnectionError(err, request=request) 781s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s The above exception was the direct cause of the following exception: 781s 781s Traceback (most recent call last): 781s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 781s job._runner( 781s ~~~~~~~~~~~^ 781s jobGraph=None, 781s ^^^^^^^^^^^^^^ 781s ...<2 lines>... 781s defer=defer, 781s ^^^^^^^^^^^^ 781s ) 781s ^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 781s returnValues = self._run(jobGraph=None, fileStore=fileStore) 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 781s return self.run(fileStore) 781s ~~~~~~~~^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 781s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 781s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 781s out = apiDockerCall( 781s job, 781s ...<8 lines>... 781s demux=demux, 781s ) 781s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 781s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 781s return cls( 781s timeout=timeout, 781s ...<3 lines>... 781s **kwargs_from_env(**kwargs) 781s ) 781s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 781s self.api = APIClient(*args, **kwargs) 781s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 781s self._version = self._retrieve_server_version() 781s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 781s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 781s raise DockerException( 781s f'Error while fetching server API version: {e}' 781s ) from e 781s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 781s 781s [2026-01-30T23:48:40+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 781s <========= 781s ERROR src/importExportFileTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py'. 781s Hint: make sure your test modules/packages have valid Python names. 781s Traceback: 781s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 781s mod = import_path( 781s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 781s importlib.import_module(module_name) 781s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 781s return _bootstrap._gcd_import(name[level:], package, level) 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s :1387: in _gcd_import 781s ??? 781s :1360: in _find_and_load 781s ??? 781s :1331: in _find_and_load_unlocked 781s ??? 781s :935: in _load_unlocked 781s ??? 781s :1023: in exec_module 781s ??? 781s :488: in _call_with_frames_removed 781s ??? 781s /usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py:30: in 781s from pytest_subtests import SubTests 781s E ModuleNotFoundError: No module named 'pytest_subtests' 781s ERROR src/jobEncapsulationTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py'. 781s Hint: make sure your test modules/packages have valid Python names. 781s Traceback: 781s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 781s mod = import_path( 781s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 781s importlib.import_module(module_name) 781s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 781s return _bootstrap._gcd_import(name[level:], package, level) 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s :1387: in _gcd_import 781s ??? 781s :1360: in _find_and_load 781s ??? 781s :1331: in _find_and_load_unlocked 781s ??? 781s :935: in _load_unlocked 781s ??? 781s :1023: in exec_module 781s ??? 781s :488: in _call_with_frames_removed 781s ??? 781s /usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py:17: in 781s from toil.test.src.jobTest import fn1Test 781s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 781s from pytest_subtests import SubTests 781s E ModuleNotFoundError: No module named 'pytest_subtests' 781s ERROR src/jobTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobTest.py'. 781s Hint: make sure your test modules/packages have valid Python names. 781s Traceback: 781s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 781s mod = import_path( 781s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 781s importlib.import_module(module_name) 781s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 781s return _bootstrap._gcd_import(name[level:], package, level) 781s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 781s :1387: in _gcd_import 781s ??? 781s :1360: in _find_and_load 781s ??? 781s :1331: in _find_and_load_unlocked 781s ??? 781s :935: in _load_unlocked 781s ??? 781s :1023: in exec_module 781s ??? 781s :488: in _call_with_frames_removed 781s ??? 781s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 781s from pytest_subtests import SubTests 781s E ModuleNotFoundError: No module named 'pytest_subtests' 781s = 13 failed, 226 passed, 136 skipped, 3 errors, 24 subtests passed in 310.91s (0:05:10) = 782s autopkgtest [23:52:59]: test pybuild-autopkgtest: -----------------------] 782s autopkgtest [23:52:59]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 782s pybuild-autopkgtest FAIL non-zero exit status 25 782s autopkgtest [23:52:59]: @@@@@@@@@@@@@@@@@@@@ summary 782s smoke-test PASS (superficial) 782s pybuild-autopkgtest FAIL non-zero exit status 25